Variant report

Variant	rs12790660
Chromosome Location	chr11:57667222-57667223
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	chr11:57666728..57668740-chr11:57669401..57671347,2	MCF-7	breast:
2	chr11:57666968..57668868-chr11:57669771..57671757,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10792112	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10896656	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896661	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896662	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229130	0.84[AFR][1000 genomes]
rs11229131	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11229148	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11229160	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11570190	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs11570195	0.90[LWK][hapmap]
rs11601320	0.81[CEU][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11605731	0.82[CEU][hapmap];0.90[YRI][hapmap]
rs11607056	1.00[ASW][hapmap];0.82[CEU][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap]
rs12360939	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12790525	0.89[YRI][hapmap]
rs12798206	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12807250	0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12807357	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1376489	0.90[LWK][hapmap];0.90[YRI][hapmap]
rs1647405	0.82[CEU][hapmap];0.93[MEX][hapmap]
rs2509808	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2847308	0.82[CEU][hapmap];0.93[MEX][hapmap]
rs576859	0.82[CEU][hapmap];0.93[MEX][hapmap]
rs589914	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs631791	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs641325	0.86[EUR][1000 genomes]
rs644883	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6591434	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs674094	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs682503	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs708228	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7117205	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71484468	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7930102	0.90[LWK][hapmap];0.90[YRI][hapmap]
rs7932091	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7936998	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9420	0.86[MEX][hapmap]
rs9645687	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12790660	MS4A7	cis	parietal	SCAN
rs12790660	MED19	cis	cerebellum	SCAN
rs12790660	PRG3	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57660600-57671200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:57664600-57672000	Weak transcription	Right Atrium	heart
3	chr11:57666000-57667800	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr11:57666200-57668400	Enhancers	K562	blood
5	chr11:57666200-57670800	Enhancers	NHEK	skin
6	chr11:57666200-57673000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr11:57666200-57673200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:57666400-57667400	Enhancers	Stomach Mucosa	stomach
9	chr11:57666400-57668400	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr11:57666400-57669200	Enhancers	Fetal Intestine Large	intestine
11	chr11:57666400-57671200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:57666400-57671200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:57666400-57672000	Enhancers	HMEC	breast
14	chr11:57666600-57667800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr11:57666800-57667600	Enhancers	Colonic Mucosa	Colon
16	chr11:57666800-57667600	Enhancers	Duodenum Mucosa	Duodenum
17	chr11:57666800-57667800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:57666800-57672000	Enhancers	Fetal Intestine Small	intestine
19	chr11:57667200-57667800	Weak transcription	Esophagus	oesophagus

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