Variant report

Variant	rs6806059
Chromosome Location	chr3:48564507-48564508
allele	A/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	chr3:48564465-48564697	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:48564368-48564679	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:48564272-48564710	U87	brain:	n/a	n/a
4	POLR2A	chr3:48564349-48564555	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:48564433-48564659	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PFKFB4	TF binding region

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1003649	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap]
rs10049154	0.84[ASN][1000 genomes]
rs10470687	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11706983	0.83[GIH][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap]
rs12107252	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12107418	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13060933	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13062576	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13063312	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13064619	0.84[ASN][1000 genomes]
rs13070798	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13091944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13094578	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13100178	0.88[ASN][1000 genomes]
rs13319635	0.92[ASN][1000 genomes]
rs13319651	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13324142	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13434258	0.83[GIH][hapmap]
rs17080289	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap]
rs2006871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276850	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276852	0.80[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2286652	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2302295	1.00[JPT][hapmap]
rs2310996	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2854394	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2854395	0.86[ASN][1000 genomes]
rs28563843	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28581474	0.85[ASN][1000 genomes]
rs28881595	0.82[ASN][1000 genomes]
rs35064573	0.83[GIH][hapmap]
rs35562294	0.91[ASN][1000 genomes]
rs3755819	0.94[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	1.00[JPT][hapmap]
rs3821876	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3969942	0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4075082	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6442126	0.86[CHB][hapmap]
rs6442127	0.86[ASN][1000 genomes]
rs6765317	0.82[ASN][1000 genomes]
rs6773261	1.00[JPT][hapmap]
rs6781283	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6785845	0.84[ASN][1000 genomes]
rs6792156	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[ASN][1000 genomes]
rs6792525	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6809981	0.83[ASN][1000 genomes]
rs740787	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7428949	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7434077	0.89[CHB][hapmap];0.90[CHD][hapmap];0.88[ASN][1000 genomes]
rs7434107	0.88[ASN][1000 genomes]
rs7620853	1.00[JPT][hapmap]
rs7623614	0.88[ASN][1000 genomes]
rs7631574	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7640031	0.88[ASN][1000 genomes]
rs7644771	0.88[ASN][1000 genomes]
rs9810549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9810991	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9811318	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9812200	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9814951	0.85[GIH][hapmap]
rs9816942	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9821797	1.00[JPT][hapmap]
rs9822677	0.84[ASN][1000 genomes]
rs9830581	0.90[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9835827	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9835902	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.86[ASN][1000 genomes]
rs9836462	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9837687	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs9841602	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9843316	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9848824	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9849280	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851743	0.88[ASN][1000 genomes]
rs9851771	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs9864729	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9869698	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9871180	1.00[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9871608	0.88[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap]
rs9875911	1.00[GIH][hapmap]
rs9878950	0.86[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.92[ASN][1000 genomes]
rs9881877	0.93[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[ASN][1000 genomes]
rs9882549	0.83[GIH][hapmap]
rs9882962	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][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	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats 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 miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48542800-48569800	Weak transcription	Right Atrium	heart
2	chr3:48545200-48572400	Weak transcription	Brain Angular Gyrus	brain
3	chr3:48545400-48565400	Weak transcription	Pancreas	Pancrea
4	chr3:48545400-48572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:48545400-48572600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:48545600-48570600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:48545600-48571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:48545600-48572600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:48552800-48572600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:48554000-48573000	Weak transcription	Right Ventricle	heart
12	chr3:48554200-48565000	Strong transcription	Fetal Intestine Small	intestine
13	chr3:48554200-48572600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:48554200-48572600	Weak transcription	Dnd41	blood
15	chr3:48554400-48572600	Weak transcription	Aorta	Aorta
16	chr3:48554800-48566400	Strong transcription	Fetal Brain Female	brain
17	chr3:48554800-48570800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr3:48555200-48582200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:48555400-48565800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:48555400-48572600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:48555400-48578000	Strong transcription	HepG2	liver
22	chr3:48555600-48567800	Weak transcription	NH-A	brain
23	chr3:48555800-48568000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:48556000-48568400	Strong transcription	HMEC	breast
25	chr3:48556200-48572600	Weak transcription	Colonic Mucosa	Colon
26	chr3:48556200-48580400	Weak transcription	HSMMtube	muscle
27	chr3:48556200-48586800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:48556400-48586400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:48557000-48572400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:48557000-48572800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:48557200-48566400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:48557200-48570000	Weak transcription	Brain Anterior Caudate	brain
33	chr3:48557200-48571400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:48557200-48572000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:48557200-48572600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:48558200-48572600	Weak transcription	Fetal Lung	lung
37	chr3:48558400-48572800	Weak transcription	HSMM	muscle
38	chr3:48558600-48566200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:48558600-48572400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:48558600-48572600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:48558600-48572600	Weak transcription	Esophagus	oesophagus
42	chr3:48558800-48569200	Weak transcription	Brain Substantia Nigra	brain
43	chr3:48559400-48575200	Weak transcription	Small Intestine	intestine
44	chr3:48559600-48571800	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:48559600-48572600	Weak transcription	Gastric	stomach
46	chr3:48559600-48586400	Weak transcription	Primary B cells from cord blood	blood
47	chr3:48559800-48572600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:48560200-48564600	Weak transcription	Fetal Intestine Large	intestine
49	chr3:48560200-48564800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:48560200-48572800	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links