Variant report

Variant	rs9461245
Chromosome Location	chr6:26354572-26354573
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	FOXA1	chr6:26354417-26354805	HepG2	liver:	n/a	n/a
2	HNF4A	chr6:26354430-26354761	HepG2	liver:	n/a	n/a
3	FOXA1	chr6:26354347-26354841	HepG2	liver:	n/a	n/a
4	FOXA1	chr6:26354326-26354779	HepG2	liver:	n/a	n/a
5	FOXA1	chr6:26354364-26354722	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26350529..26353058-chr6:26354416..26356563,2	K562	blood:
2	chr6:26352176..26356420-chr6:26519489..26524545,4	K562	blood:
3	chr6:26352931..26356420-chr6:26520848..26524138,3	K562	blood:

Variant related genes	Relation type
RNU6-1259P	TF binding region
ENSG00000199289	Chromatin interaction
ENSG00000228223	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10807008	0.81[ASW][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap]
rs10946824	1.00[CHD][hapmap]
rs10946826	1.00[CHD][hapmap]
rs10946829	1.00[CHD][hapmap]
rs1131936	0.85[CEU][hapmap]
rs12191917	1.00[CHD][hapmap]
rs12194001	1.00[CHB][hapmap]
rs12196371	0.91[YRI][hapmap]
rs12201546	1.00[CHD][hapmap]
rs12203176	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205476	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12206621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206812	1.00[CHD][hapmap]
rs12207930	1.00[CHD][hapmap]
rs12208788	0.85[CEU][hapmap]
rs12214444	1.00[CHD][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap]
rs12214924	1.00[CHD][hapmap]
rs12664899	0.85[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs14232	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs17537465	0.85[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17539219	1.00[CHD][hapmap]
rs17610161	1.00[CHD][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.81[YRI][hapmap]
rs2393652	1.00[CHD][hapmap]
rs2893845	1.00[CHD][hapmap]
rs2893847	1.00[CHD][hapmap]
rs2893848	1.00[CHD][hapmap]
rs35183513	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799378	0.81[ASW][hapmap]
rs3846843	1.00[CHD][hapmap]
rs3846848	1.00[CHD][hapmap]
rs3902051	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap]
rs41266835	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4609015	1.00[CHD][hapmap]
rs4711108	0.84[CEU][hapmap];0.91[YRI][hapmap]
rs4711110	0.92[YRI][hapmap]
rs4712982	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712986	0.85[CEU][hapmap]
rs4712988	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap]
rs4712989	0.82[AFR][1000 genomes]
rs4712990	0.81[ASW][hapmap];1.00[CHD][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap]
rs4712993	1.00[CHD][hapmap]
rs4712994	1.00[CHD][hapmap]
rs4712996	1.00[CHD][hapmap]
rs4712999	1.00[CHB][hapmap]
rs55827419	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55984635	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56023587	0.82[AFR][1000 genomes]
rs56380525	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456715	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456716	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456718	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900725	1.00[CHD][hapmap]
rs6914931	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6920986	1.00[CHD][hapmap]
rs6926878	1.00[CHD][hapmap]
rs72836457	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72836479	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72841510	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72841540	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7355	0.85[CEU][hapmap]
rs7356849	0.85[CEU][hapmap]
rs7744254	1.00[CHD][hapmap]
rs7751280	1.00[CHD][hapmap]
rs7768108	1.00[CHD][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap]
rs7770214	1.00[CHD][hapmap]
rs9104	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes]
rs9467716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467717	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467718	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467723	0.81[EUR][1000 genomes]
rs9688949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv5230	chr6:26321593-26361531	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv3521788	chr6:26334022-26356973	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3521789	chr6:26334022-26356973	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9461245	GMNN	cis	parietal	SCAN
rs9461245	BTN3A1	cis	parietal	SCAN
rs9461245	BTN3A2	cis	parietal	SCAN
rs9461245	BTN3A1	Cis_1M	lymphoblastoid	RTeQTL
rs9461245	BTN2A2	Cis_1M	lymphoblastoid	RTeQTL
rs9461245	BTN2A2	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26348000-26355600	Weak transcription	Fetal Thymus	thymus
2	chr6:26348600-26354800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:26350800-26354600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:26351600-26355600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:26352600-26354600	Weak transcription	NHLF	lung
6	chr6:26352600-26364200	Weak transcription	NHEK	skin
7	chr6:26352800-26355200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:26352800-26364000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:26353000-26364200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:26353200-26355200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:26353600-26356600	Enhancers	HepG2	liver
12	chr6:26353800-26355400	Enhancers	K562	blood
13	chr6:26354000-26354600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:26354200-26355200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:26354200-26355600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr6:26354200-26355800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:26354400-26354600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:26354400-26354600	Enhancers	Fetal Intestine Small	intestine
19	chr6:26354400-26354600	Enhancers	A549	lung
20	chr6:26354400-26355200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr6:26354400-26355600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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