Variant report

Variant	rs7629936
Chromosome Location	chr3:49836707-49836708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:49836705-49836791	K562	blood:	n/a	n/a
2	EGR1	chr3:49836657-49836824	K562	blood:	n/a	n/a
3	POLR2A	chr3:49836679-49836742	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49828367..49831319-chr3:49832750..49837135,3	MCF-7	breast:
2	chr3:49822443..49824748-chr3:49834059..49836824,2	K562	blood:
3	chr3:49835114..49838114-chr3:49838714..49841176,3	K562	blood:
4	chr3:49830703..49832221-chr3:49836417..49838568,2	K562	blood:
5	chr3:49830703..49832538-chr3:49835822..49838568,4	K562	blood:
6	chr3:49828847..49830449-chr3:49834331..49837009,2	K562	blood:

No data

Variant related genes	Relation type
FAM212A	TF binding region
ENSG00000185614	Chromatin interaction
ENSG00000187492	Chromatin interaction
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10049413	0.90[ASN][1000 genomes]
rs1049256	0.90[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs10865958	0.93[ASN][1000 genomes]
rs10865959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11130214	0.87[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11130216	0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[YRI][hapmap];0.87[ASN][1000 genomes]
rs11130218	0.96[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11130219	0.96[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11130221	0.88[ASN][1000 genomes]
rs1128535	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11709573	0.89[CHB][hapmap]
rs11709680	0.96[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11710675	0.89[ASN][1000 genomes]
rs11714957	0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.92[ASN][1000 genomes]
rs11715304	0.95[ASN][1000 genomes]
rs11716575	0.96[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11717256	0.94[ASN][1000 genomes]
rs11717463	0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs11920900	0.93[ASN][1000 genomes]
rs12381242	0.86[ASN][1000 genomes]
rs12490656	0.83[ASN][1000 genomes]
rs12496226	0.82[ASN][1000 genomes]
rs13063621	0.88[ASN][1000 genomes]
rs13084243	0.92[ASN][1000 genomes]
rs13085679	0.93[ASN][1000 genomes]
rs13086130	0.92[ASN][1000 genomes]
rs13086465	0.89[ASN][1000 genomes]
rs13090611	0.85[ASN][1000 genomes]
rs1317140	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap];0.86[ASN][1000 genomes]
rs13316065	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1491986	0.96[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs17657664	0.89[CHB][hapmap]
rs17657688	0.89[CHB][hapmap]
rs1799843	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1799845	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2234385	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2234391	0.81[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2246832	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2247036	0.90[ASN][1000 genomes]
rs2271960	0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2271961	0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2276864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2291542	0.87[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.89[ASN][1000 genomes]
rs2307021	0.90[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2352967	0.91[ASN][1000 genomes]
rs2352969	0.89[CHB][hapmap]
rs2352974	0.81[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2352975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2352984	0.89[CHB][hapmap]
rs2624819	0.89[CHB][hapmap]
rs2624821	0.89[CHB][hapmap]
rs2681779	0.89[CHB][hapmap]
rs34451146	0.88[ASN][1000 genomes]
rs34522271	0.92[ASN][1000 genomes]
rs34614773	0.86[ASN][1000 genomes]
rs34735338	0.94[ASN][1000 genomes]
rs35210174	0.90[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35261599	0.96[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs35474403	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3749237	0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.92[ASN][1000 genomes]
rs3749240	0.90[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs3749241	0.88[ASN][1000 genomes]
rs3774759	0.89[CHB][hapmap]
rs3811695	0.84[ASN][1000 genomes]
rs3811696	0.86[ASN][1000 genomes]
rs3819325	0.87[ASN][1000 genomes]
rs4519692	0.86[ASN][1000 genomes]
rs4768	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.89[ASN][1000 genomes]
rs4855841	0.83[ASN][1000 genomes]
rs4855850	0.86[ASN][1000 genomes]
rs4855862	0.96[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4855867	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs57648519	0.88[ASN][1000 genomes]
rs59906301	0.87[ASN][1000 genomes]
rs60205400	0.88[ASN][1000 genomes]
rs62260715	0.94[ASN][1000 genomes]
rs62260719	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62260729	0.90[ASN][1000 genomes]
rs6446295	0.90[ASN][1000 genomes]
rs6766836	0.88[ASN][1000 genomes]
rs6774354	0.89[CHB][hapmap]
rs6775384	0.81[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6785549	0.96[CHD][hapmap];0.83[GIH][hapmap];0.83[ASN][1000 genomes]
rs6802890	0.81[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs6804655	0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[YRI][hapmap];0.87[ASN][1000 genomes]
rs695238	0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs71324996	0.89[ASN][1000 genomes]
rs7372725	0.82[ASN][1000 genomes]
rs7372730	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs7372966	0.95[CHD][hapmap];0.83[GIH][hapmap];0.82[ASN][1000 genomes]
rs7374183	0.95[CHD][hapmap];0.83[GIH][hapmap];0.82[ASN][1000 genomes]
rs7374277	0.82[ASN][1000 genomes]
rs7429353	0.82[ASN][1000 genomes]
rs7431078	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7431106	0.95[CHD][hapmap];0.80[GIH][hapmap];0.88[ASN][1000 genomes]
rs7615206	0.89[CHB][hapmap]
rs7618501	0.89[ASN][1000 genomes]
rs7618519	0.90[ASN][1000 genomes]
rs7627864	0.89[CHB][hapmap]
rs7634886	0.86[ASN][1000 genomes]
rs7634902	0.90[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7645061	0.81[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7648987	0.81[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7649348	0.90[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs868891	0.89[CHB][hapmap]
rs9814765	0.86[ASN][1000 genomes]
rs9815766	0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs9819511	0.90[ASN][1000 genomes]
rs9850465	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9853458	0.86[ASN][1000 genomes]
rs9855505	0.95[CHD][hapmap];0.83[GIH][hapmap];0.82[ASN][1000 genomes]
rs9859153	0.96[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs9865480	0.86[ASN][1000 genomes]
rs9871654	0.90[ASN][1000 genomes]
rs9872864	0.95[CHD][hapmap];0.83[GIH][hapmap];0.82[ASN][1000 genomes]
rs9873183	0.81[ASN][1000 genomes]
rs9876508	0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs9882639	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7629936	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs7629936	CSPG5	cis	cerebellum	SCAN
rs7629936	AMT	cis	cerebellum	SCAN
rs7629936	CCDC71	cis	cerebellum	SCAN
rs7629936	IP6K2	cis	cerebellum	SCAN
rs7629936	RNF123	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49825600-49840000	Weak transcription	Spleen	Spleen
2	chr3:49833200-49838800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49833400-49836800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:49833400-49838800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:49835200-49839800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:49836200-49837400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:49836200-49838600	Enhancers	HepG2	liver
8	chr3:49836400-49836800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:49836400-49836800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:49836400-49836800	Enhancers	Hela-S3	cervix
11	chr3:49836400-49837400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:49836400-49837600	Enhancers	Esophagus	oesophagus
13	chr3:49836400-49837600	Enhancers	HMEC	breast
14	chr3:49836600-49836800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:49836600-49836800	Enhancers	A549	lung
16	chr3:49836600-49837200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr3:49836600-49837400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr3:49836600-49837600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:49836600-49837600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:49836600-49837600	Enhancers	HSMM	muscle
21	chr3:49836600-49837600	Enhancers	NHDF-Ad	bronchial
22	chr3:49836600-49837800	Enhancers	Stomach Mucosa	stomach
23	chr3:49836600-49838000	Enhancers	Placenta Amnion	Placenta Amnion

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