Variant report

Variant	rs247776
Chromosome Location	chr19:19842615-19842616
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19626852..19628495-chr19:19842334..19845203,2	MCF-7	breast:
2	chr19:19842192..19843794-chr19:19857515..19860071,2	K562	blood:
3	chr19:19772731..19775725-chr19:19841970..19845590,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105726	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000258674	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1061270	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12972505	0.98[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12973901	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12980676	0.80[ASN][1000 genomes]
rs12982273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12984272	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12984880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12986120	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17699333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1978716	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2013561	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2163813	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2315285	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247770	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247771	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs247772	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs247773	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs247774	0.96[ASN][1000 genomes]
rs247778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247780	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34352974	0.80[ASN][1000 genomes]
rs34984663	0.80[ASN][1000 genomes]
rs36006965	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56093876	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74181153	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1065704	chr19:19797999-19865818	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv543929	chr19:19797999-19865818	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1062017	chr19:19803482-19865818	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv543930	chr19:19803482-19865818	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1057601	chr19:19803482-19873623	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1063535	chr19:19806386-19863631	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers 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	10 gene(s)	inside rSNPs	diseases
10	nsv1062212	chr19:19806386-19869332	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1060122	chr19:19814678-19879575	Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv2436	chr19:19815858-19869171	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv911311	chr19:19831544-19863284	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19828400-19843200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:19831200-19843000	Weak transcription	NH-A	brain
3	chr19:19836600-19842800	Weak transcription	Osteobl	bone
4	chr19:19837200-19842800	ZNF genes & repeats	Fetal Intestine Small	intestine
5	chr19:19837400-19842800	ZNF genes & repeats	Fetal Brain Female	brain
6	chr19:19837800-19842800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:19838000-19842800	ZNF genes & repeats	Brain Germinal Matrix	brain
8	chr19:19838600-19842800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr19:19838800-19842800	Weak transcription	Psoas Muscle	Psoas
10	chr19:19838800-19842800	Weak transcription	K562	blood
11	chr19:19839600-19842800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
12	chr19:19839800-19842800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:19840000-19842800	Weak transcription	NHLF	lung
14	chr19:19840400-19843000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:19840400-19843200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:19840400-19843200	Weak transcription	Gastric	stomach
17	chr19:19840600-19842800	Weak transcription	Colon Smooth Muscle	Colon
18	chr19:19840600-19842800	Weak transcription	Ovary	ovary
19	chr19:19840600-19844400	ZNF genes & repeats	Liver	Liver
20	chr19:19840800-19842800	Weak transcription	Fetal Heart	heart
21	chr19:19840800-19842800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr19:19840800-19842800	Weak transcription	NHEK	skin
23	chr19:19841000-19842800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:19841000-19842800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:19841000-19842800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:19841200-19842800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:19841200-19842800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:19841200-19842800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:19841200-19842800	Weak transcription	HMEC	breast
30	chr19:19841200-19843000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:19841400-19842800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:19841400-19842800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:19841400-19842800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:19841600-19842800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr19:19841800-19842800	Weak transcription	Brain Substantia Nigra	brain
36	chr19:19841800-19843000	Enhancers	Primary B cells from peripheral blood	blood
37	chr19:19842000-19842800	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr19:19842000-19842800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:19842000-19843000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:19842000-19843000	Enhancers	Lung	lung
41	chr19:19842000-19844400	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr19:19842200-19842800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr19:19842200-19842800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:19842200-19842800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr19:19842200-19842800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:19842200-19842800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr19:19842400-19842800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr19:19842400-19842800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:19842400-19842800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:19842400-19842800	Active TSS	Brain Angular Gyrus	brain

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