Variant report

Variant	rs8102799
Chromosome Location	chr19:53602953-53602954
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	chr19:53601090..53603099-chr19:53630653..53632192,2	MCF-7	breast:
2	chr19:53601358..53604101-chr19:53630122..53631842,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10402901	1.00[CHB][hapmap]
rs10406237	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407043	0.91[MEX][hapmap]
rs10409615	1.00[ASN][1000 genomes]
rs10410030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412805	1.00[ASN][1000 genomes]
rs10418505	1.00[ASN][1000 genomes]
rs12971916	1.00[CHB][hapmap]
rs12982323	1.00[CHB][hapmap]
rs1661923	1.00[CHB][hapmap]
rs16984438	1.00[CHB][hapmap];0.92[MKK][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs16984443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16984486	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28368410	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28528321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661145	1.00[ASN][1000 genomes]
rs28662846	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28691095	1.00[ASN][1000 genomes]
rs28701520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28726276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58143828	1.00[ASN][1000 genomes]
rs6509725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253566	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935216	1.00[ASN][1000 genomes]
rs73935236	1.00[ASN][1000 genomes]
rs8099848	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100134	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109900	1.00[CHB][hapmap]
rs8110394	1.00[CHB][hapmap]
rs8113824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:37 , 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	nsv9748	chr19:53599536-53603017	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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
31	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
32	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
33	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
34	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
35	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
36	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
37	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8102799	ZSCAN4	cis	cerebellum	SCAN
rs8102799	LILRB3	cis	parietal	SCAN
rs8102799	ZNF444	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53573600-53604800	Weak transcription	Hela-S3	cervix
2	chr19:53576800-53605200	Weak transcription	Stomach Mucosa	stomach
3	chr19:53585400-53604800	Weak transcription	Psoas Muscle	Psoas
4	chr19:53586400-53603400	Strong transcription	Primary T cells from cord blood	blood
5	chr19:53588400-53603400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr19:53589200-53604800	Weak transcription	Fetal Brain Male	brain
7	chr19:53589600-53604800	Weak transcription	Small Intestine	intestine
8	chr19:53590400-53605000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:53592800-53604800	Weak transcription	HUVEC	blood vessel
10	chr19:53594400-53603400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:53594400-53605200	Weak transcription	Fetal Lung	lung
12	chr19:53594600-53604800	Weak transcription	Fetal Kidney	kidney
13	chr19:53594600-53604800	Weak transcription	NHEK	skin
14	chr19:53595200-53603000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:53595200-53604000	Weak transcription	Pancreas	Pancrea
16	chr19:53596600-53603200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr19:53597600-53604800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr19:53597800-53604800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:53597800-53604800	Weak transcription	NH-A	brain
20	chr19:53598800-53604800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:53599000-53604800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr19:53599000-53604800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr19:53599000-53604800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:53599000-53604800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:53599000-53604800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:53599000-53604800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:53599000-53604800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr19:53599000-53604800	Weak transcription	HSMM	muscle
29	chr19:53599000-53605000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr19:53599000-53605400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:53599200-53604800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:53599200-53604800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:53600000-53603200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:53600400-53603400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr19:53600600-53603400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:53600600-53603400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
37	chr19:53600600-53603400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr19:53600600-53603400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:53600600-53603600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:53600600-53603800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:53600800-53603000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:53600800-53603000	Strong transcription	Dnd41	blood
43	chr19:53600800-53603200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:53600800-53603200	Strong transcription	Liver	Liver
45	chr19:53600800-53603200	Strong transcription	Colonic Mucosa	Colon
46	chr19:53600800-53603200	Strong transcription	Fetal Muscle Leg	muscle
47	chr19:53600800-53603200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr19:53600800-53603200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr19:53600800-53603200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr19:53600800-53603400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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