Variant report

Variant	rs13006131
Chromosome Location	chr2:46608542-46608543
allele	C/G
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	POLR2A	chr2:46608508-46608603	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:46602784-46612387	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:46602319-46619222	K562	blood:	n/a	n/a
4	POLR2A	chr2:46608015-46608733	K562	blood:	n/a	n/a
5	POLR2A	chr2:46608500-46608758	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:46607914-46608962	K562	blood:	n/a	n/a
7	POLR2A	chr2:46608448-46608913	HepG2	liver:	n/a	n/a
8	FOSL2	chr2:46606590-46610589	HepG2	liver:	n/a	chr2:46608863-46608870 chr2:46608862-46608871
9	POLR2A	chr2:46606423-46612176	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
EPAS1	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10178633	0.81[CEU][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes]
rs11675232	0.92[CEU][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11675328	0.86[AMR][1000 genomes]
rs11675441	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11678465	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11678817	0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11681242	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11686705	0.88[AMR][1000 genomes]
rs11690951	0.93[CEU][hapmap];0.81[CHB][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11691694	0.86[AMR][1000 genomes]
rs11692911	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11693596	0.85[AMR][1000 genomes]
rs11693754	0.88[AMR][1000 genomes]
rs11694193	0.96[CEU][hapmap];0.85[CHB][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12467821	0.89[CEU][hapmap]
rs13019268	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1530622	0.85[CEU][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1868092	0.85[CEU][hapmap];0.94[MEX][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1868093	0.85[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1868094	0.85[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35145595	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768730	0.85[CEU][hapmap]
rs4953359	0.80[CEU][hapmap]
rs55826825	0.89[AMR][1000 genomes]
rs56161503	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59034065	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62138871	0.88[AMR][1000 genomes]
rs7557402	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7567582	1.00[CEU][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7568285	0.81[CEU][hapmap]
rs7571218	0.93[GIH][hapmap]
rs7583088	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7583392	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7591548	0.89[AMR][1000 genomes]
rs7594278	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7594912	0.81[CEU][hapmap];0.90[GIH][hapmap]
rs7598371	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7606559	0.92[CEU][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
2	chr2:46574800-46613000	Weak transcription	HSMM	muscle
3	chr2:46589800-46616600	Weak transcription	Thymus	Thymus
4	chr2:46592200-46619800	Weak transcription	K562	blood
5	chr2:46592600-46611200	Weak transcription	Primary T cells from cord blood	blood
6	chr2:46592600-46612600	Strong transcription	NHEK	skin
7	chr2:46592600-46616200	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr2:46593600-46615400	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:46594000-46612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:46594400-46615600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr2:46594600-46612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:46594800-46615400	Strong transcription	Liver	Liver
13	chr2:46594800-46615600	Strong transcription	HUVEC	blood vessel
14	chr2:46595000-46616000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:46596000-46612800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:46600600-46612600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:46600800-46609200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:46600800-46614200	Strong transcription	HepG2	liver
19	chr2:46601800-46616400	Genic enhancers	Placenta	Placenta
20	chr2:46602000-46609800	Strong transcription	Small Intestine	intestine
21	chr2:46602000-46616000	Strong transcription	Pancreas	Pancrea
22	chr2:46602400-46608800	Strong transcription	Spleen	Spleen
23	chr2:46602400-46613400	Strong transcription	Fetal Intestine Small	intestine
24	chr2:46603200-46614200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:46604000-46608600	Strong transcription	Fetal Intestine Large	intestine
26	chr2:46604000-46609000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:46604400-46608800	Genic enhancers	NHLF	lung
28	chr2:46604600-46612000	Strong transcription	Aorta	Aorta
29	chr2:46605000-46613000	Strong transcription	A549	lung
30	chr2:46605200-46608600	Genic enhancers	Esophagus	oesophagus
31	chr2:46605200-46614200	Weak transcription	Brain Substantia Nigra	brain
32	chr2:46605400-46609000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:46605600-46614800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr2:46606000-46612200	Strong transcription	Colonic Mucosa	Colon
35	chr2:46606000-46615000	Strong transcription	Right Ventricle	heart
36	chr2:46606000-46615400	Strong transcription	Left Ventricle	heart
37	chr2:46606200-46613000	Weak transcription	Right Atrium	heart
38	chr2:46606200-46613400	Strong transcription	Gastric	stomach
39	chr2:46606400-46611200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:46606600-46613000	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:46606600-46614600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:46606800-46609800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:46606800-46613000	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:46607000-46609800	Strong transcription	Fetal Muscle Leg	muscle
45	chr2:46607000-46612600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:46607000-46612600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:46607000-46613000	Weak transcription	Brain Anterior Caudate	brain
48	chr2:46607000-46613800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr2:46607000-46617000	Weak transcription	Stomach Mucosa	stomach
50	chr2:46607200-46609400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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