Variant report

Variant	rs55959943
Chromosome Location	chr19:53620111-53620112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53618140..53620226-chr19:53631544..53634250,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170954	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10414845	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10417212	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10417706	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10418143	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10418422	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10418793	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11879860	0.95[ASN][1000 genomes]
rs11879862	0.95[ASN][1000 genomes]
rs13344987	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13346801	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16984484	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16984492	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28456040	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28692585	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28845271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3786524	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55767820	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55816705	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58014188	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59504768	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59780072	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7248648	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7251341	0.93[ASN][1000 genomes]
rs7252862	0.95[ASN][1000 genomes]
rs7259388	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7259392	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7259819	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7259824	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:43 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
12	nsv580068	chr19:53594806-53623771	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv912343	chr19:53594806-53632896	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv580069	chr19:53599618-53626513	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv912344	chr19:53599618-53632896	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv435700	chr19:53600132-53631014	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv2488809	chr19:53600824-53632050	Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv527053	chr19:53600845-53626112	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv458758	chr19:53600845-53626112	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	nsv580070	chr19:53600845-53626112	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	nsv912345	chr19:53600845-53626112	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
22	nsv458759	chr19:53600845-53626513	Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
23	nsv470153	chr19:53600845-53626513	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
24	nsv580071	chr19:53600845-53626513	Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
25	nsv458760	chr19:53600845-53627777	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
26	nsv580072	chr19:53600845-53627777	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
27	nsv580073	chr19:53600845-53632896	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
28	nsv912346	chr19:53600845-53632896	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
29	esv3328253	chr19:53601573-53631676	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
30	nsv580074	chr19:53601649-53627777	Strong transcription Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
31	esv3319060	chr19:53602306-53632301	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
32	esv3319061	chr19:53602306-53632301	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
33	esv3346626	chr19:53602317-53629991	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
34	esv8151	chr19:53602331-53632603	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
35	nsv515862	chr19:53602953-53626513	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
36	nsv912347	chr19:53602953-53632896	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
37	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
38	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
39	nsv580075	chr19:53603590-53626112	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
40	nsv580076	chr19:53603590-53626513	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
41	nsv1061016	chr19:53603952-53641569	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
42	nsv912348	chr19:53605047-53632896	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
43	nsv912349	chr19:53612855-53627777	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53607400-53630600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:53607600-53620600	Weak transcription	Stomach Mucosa	stomach
3	chr19:53607600-53635000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:53610200-53620600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr19:53611200-53621200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:53612600-53634200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:53613000-53620400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:53613000-53620800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:53613000-53629600	Weak transcription	Fetal Heart	heart
10	chr19:53613000-53634600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:53613000-53635400	Weak transcription	HSMMtube	muscle
12	chr19:53614400-53621000	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr19:53615200-53620200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr19:53615200-53620200	Strong transcription	Dnd41	blood
15	chr19:53615400-53620600	Strong transcription	Fetal Brain Female	brain
16	chr19:53615400-53620600	Strong transcription	Left Ventricle	heart
17	chr19:53615400-53621000	Strong transcription	Fetal Lung	lung
18	chr19:53615400-53621400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:53615600-53620400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:53615800-53622800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:53616000-53620400	Strong transcription	Osteobl	bone
22	chr19:53616000-53620600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr19:53616000-53634600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:53616000-53635000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:53616800-53620400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr19:53617600-53620600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:53617600-53622800	ZNF genes & repeats	Fetal Intestine Large	intestine
28	chr19:53617800-53621800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:53618200-53620800	Weak transcription	Fetal Brain Male	brain
30	chr19:53618400-53625600	Weak transcription	Gastric	stomach
31	chr19:53618600-53620400	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr19:53618600-53621400	ZNF genes & repeats	Primary B cells from cord blood	blood
33	chr19:53618600-53634400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr19:53618800-53620400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
35	chr19:53618800-53620800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr19:53618800-53620800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:53618800-53627800	Weak transcription	Thymus	Thymus
38	chr19:53618800-53634000	Weak transcription	Pancreas	Pancrea
39	chr19:53619000-53620800	Weak transcription	Colonic Mucosa	Colon
40	chr19:53619000-53625600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:53619000-53630600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr19:53619200-53621200	ZNF genes & repeats	Brain Germinal Matrix	brain
43	chr19:53619200-53621800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr19:53619200-53625600	Weak transcription	Spleen	Spleen
45	chr19:53619400-53620200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:53619400-53625800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:53619400-53627200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr19:53619400-53634400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:53619400-53634400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:53619600-53620200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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