Variant report

Variant	rs6976053
Chromosome Location	chr7:100512119-100512120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:100507577..100512312-chr7:100514268..100518722,4	K562	blood:
2	chr7:100486728..100489422-chr7:100510624..100512733,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176125	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1054391	0.92[CEU][hapmap]
rs10953305	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11973000	0.81[ASN][1000 genomes]
rs12666785	0.89[CEU][hapmap]
rs12669120	0.96[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12672665	0.92[CEU][hapmap]
rs12705094	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13226043	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13232524	0.97[ASN][1000 genomes]
rs13241786	0.82[CEU][hapmap]
rs15624	0.92[CEU][hapmap]
rs2405975	0.95[ASN][1000 genomes]
rs2894713	0.81[ASN][1000 genomes]
rs3087504	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs314368	0.83[EUR][1000 genomes]
rs314371	0.86[EUR][1000 genomes]
rs314372	0.86[EUR][1000 genomes]
rs314374	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs314375	0.92[CEU][hapmap]
rs314376	0.96[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs314377	0.92[CEU][hapmap]
rs314378	0.92[CEU][hapmap]
rs34005963	0.92[ASN][1000 genomes]
rs3847063	0.93[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3847068	0.81[ASN][1000 genomes]
rs3931823	0.81[ASN][1000 genomes]
rs4727469	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4727470	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729615	0.92[CEU][hapmap]
rs4729616	0.89[CEU][hapmap]
rs4729617	0.92[CEU][hapmap]
rs4729618	0.92[CEU][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap]
rs4729620	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6465776	0.92[CEU][hapmap]
rs6942607	0.96[CEU][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6954151	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7783457	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7801015	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7803865	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS 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	90 gene(s)	inside rSNPs	diseases
7	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Plasminogen activator inhibitor type 1 levels (PAI-1)	22990020	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6976053	MUC3A	cis	Liver	GTEx
rs6976053	SRRT	cis	cerebellum	SCAN
rs6976053	RELN	cis	parietal	SCAN
rs6976053	MUC3A	cis	multi-tissue	Pritchard
rs6976053	MYH16	cis	parietal	SCAN
rs6976053	C7orf59	cis	parietal	SCAN
rs6976053	MCM7	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100504200-100516400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:100507800-100513800	Weak transcription	Colonic Mucosa	Colon
3	chr7:100508400-100514000	Weak transcription	K562	blood
4	chr7:100510400-100514000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:100510400-100514200	Weak transcription	Placenta	Placenta
6	chr7:100510600-100512400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr7:100510600-100512600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr7:100511000-100512200	Enhancers	HepG2	liver
9	chr7:100511000-100513000	Enhancers	Liver	Liver
10	chr7:100511000-100513000	Enhancers	Fetal Intestine Large	intestine
11	chr7:100511000-100513000	Enhancers	Stomach Mucosa	stomach
12	chr7:100511200-100512600	Enhancers	Fetal Intestine Small	intestine
13	chr7:100511200-100512800	Enhancers	Gastric	stomach
14	chr7:100511400-100512200	Enhancers	Duodenum Mucosa	Duodenum
15	chr7:100511600-100513000	Enhancers	Pancreas	Pancrea
16	chr7:100512000-100513000	Enhancers	A549	lung

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