Variant report

Variant	rs12979860
Chromosome Location	chr19:39738787-39738788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr19:39738011-39739511	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr19:39737576-39739065	H1-hESC	embryonic stem cell:	n/a	chr19:39738397-39738407 chr19:39737917-39737926 chr19:39738538-39738550 chr19:39737763-39737772 chr19:39738396-39738406 chr19:39738322-39738331

Variant related genes	Relation type
IFNL3	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11881222	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11882871	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12971396	0.85[ASN][1000 genomes]
rs12972991	1.00[CHB][hapmap]
rs12980275	1.00[CHB][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs12982533	0.80[EUR][1000 genomes]
rs12983038	0.85[ASN][1000 genomes]
rs28416813	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803217	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803221	0.85[ASN][1000 genomes]
rs4803222	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66531907	0.85[ASN][1000 genomes]
rs68018539	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7248668	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs8099917	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs8105086	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8105790	0.88[ASN][1000 genomes]
rs8107030	0.85[ASN][1000 genomes]
rs8109889	0.83[ASN][1000 genomes]
rs8113007	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs958039	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833830	chr19:39709538-39837846	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv911678	chr19:39710903-39763765	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1796501	chr19:39723520-39740868	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
6	nsv963046	chr19:39735570-39739516	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Response to hepatitis C treatment	19684573	GWAS catalog
Chronic hepatitis C infection	23420232	GWAS catalog

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39737600-39738800	Enhancers	Primary B cells from peripheral blood	blood
2	chr19:39737600-39738800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
3	chr19:39737600-39738800	Bivalent/Poised TSS	Fetal Brain Female	brain
4	chr19:39737600-39738800	Bivalent Enhancer	Fetal Thymus	thymus
5	chr19:39737600-39739000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr19:39737600-39739000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr19:39737600-39739000	Bivalent Enhancer	Fetal Intestine Small	intestine
8	chr19:39737600-39739000	Enhancers	Gastric	stomach
9	chr19:39737600-39739000	Bivalent Enhancer	Lung	lung
10	chr19:39737600-39739000	Bivalent Enhancer	Spleen	Spleen
11	chr19:39737600-39739000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
12	chr19:39737600-39739200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr19:39737800-39738800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr19:39737800-39738800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:39737800-39738800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
16	chr19:39737800-39738800	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr19:39737800-39739000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:39737800-39739000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr19:39737800-39739000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr19:39737800-39739000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:39737800-39739000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:39737800-39739000	Bivalent Enhancer	Fetal Intestine Large	intestine
23	chr19:39737800-39739200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
24	chr19:39737800-39739400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr19:39737800-39739600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:39738000-39738800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:39738000-39738800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:39738000-39738800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:39738000-39738800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
30	chr19:39738000-39738800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr19:39738000-39738800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:39738000-39738800	Bivalent Enhancer	Fetal Brain Male	brain
33	chr19:39738000-39738800	Bivalent Enhancer	Stomach Mucosa	stomach
34	chr19:39738000-39739000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr19:39738000-39739000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr19:39738000-39739000	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr19:39738000-39739000	Enhancers	Fetal Heart	heart
38	chr19:39738000-39739000	Enhancers	Pancreas	Pancrea
39	chr19:39738000-39739000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
40	chr19:39738000-39739200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
41	chr19:39738000-39740200	Enhancers	Primary hematopoietic stem cells	blood
42	chr19:39738000-39740400	Enhancers	Liver	Liver
43	chr19:39738200-39738800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:39738200-39738800	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:39738200-39738800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
46	chr19:39738200-39739000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr19:39738200-39739000	Bivalent Enhancer	Colonic Mucosa	Colon
48	chr19:39738400-39738800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:39738400-39738800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
50	chr19:39738400-39738800	Active TSS	Primary T helper naive cells fromperipheralblood	blood

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