Variant report

Variant	rs12531900
Chromosome Location	chr7:65726928-65726929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65718957..65720490-chr7:65725606..65727154,2	MCF-7	breast:
2	chr7:65719328..65723355-chr7:65725025..65727882,3	K562	blood:
3	chr7:65723144..65728199-chr7:65728975..65732858,5	K562	blood:

Extended variants
information (count: 126 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs12530506	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12530746	0.89[EUR][1000 genomes]
rs12530898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs12531358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12532060	0.87[EUR][1000 genomes]
rs12532173	0.89[EUR][1000 genomes]
rs12532182	0.89[EUR][1000 genomes]
rs12532247	0.89[EUR][1000 genomes]
rs12532249	0.89[EUR][1000 genomes]
rs12532278	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12532327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs12532383	0.89[EUR][1000 genomes]
rs12532423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12532657	0.87[EUR][1000 genomes]
rs12532675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12533387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12533877	0.89[EUR][1000 genomes]
rs12534039	0.87[EUR][1000 genomes]
rs12534109	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12534249	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12534263	0.87[EUR][1000 genomes]
rs12534477	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12534881	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12535985	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12536816	1.00[EUR][1000 genomes]
rs12537039	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12537368	0.89[EUR][1000 genomes]
rs12537698	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12537936	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12538025	1.00[AFR][1000 genomes]
rs12538113	0.89[EUR][1000 genomes]
rs12538147	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12538379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12538686	0.81[EUR][1000 genomes]
rs12538961	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12539795	0.89[EUR][1000 genomes]
rs12540307	0.80[EUR][1000 genomes]
rs12540667	0.87[EUR][1000 genomes]
rs12540888	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1363056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2292936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2292937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35910256	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3735145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3815684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4149467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4717291	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4718342	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4718345	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4718347	0.81[EUR][1000 genomes]
rs4718350	0.89[EUR][1000 genomes]
rs4718353	0.87[EUR][1000 genomes]
rs4718354	0.89[EUR][1000 genomes]
rs62465362	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465363	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465364	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465365	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465367	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465372	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62465373	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62465376	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62465377	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62465380	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62465389	0.89[EUR][1000 genomes]
rs62465390	0.87[EUR][1000 genomes]
rs62465391	0.85[EUR][1000 genomes]
rs62465392	0.89[EUR][1000 genomes]
rs62465394	0.89[EUR][1000 genomes]
rs62465395	0.89[EUR][1000 genomes]
rs62465396	0.89[EUR][1000 genomes]
rs62465397	0.89[EUR][1000 genomes]
rs62465399	0.83[EUR][1000 genomes]
rs62465400	0.89[EUR][1000 genomes]
rs62465401	0.89[EUR][1000 genomes]
rs62465402	0.87[EUR][1000 genomes]
rs62465403	0.84[EUR][1000 genomes]
rs62465404	0.89[EUR][1000 genomes]
rs62465405	0.81[EUR][1000 genomes]
rs62465422	0.89[EUR][1000 genomes]
rs62465474	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62465475	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62465476	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62465483	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62465484	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465512	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465513	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465515	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465519	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465521	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465522	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465525	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465526	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465527	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62465542	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62465545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62465546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62465547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62465550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62467411	1.00[AFR][1000 genomes]
rs62467413	1.00[AFR][1000 genomes]
rs62467414	1.00[AFR][1000 genomes]
rs62467421	1.00[AFR][1000 genomes]
rs62467437	1.00[AFR][1000 genomes]
rs62467450	1.00[AFR][1000 genomes]
rs62468669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62468673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62468674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62468677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62468679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62468696	0.89[EUR][1000 genomes]
rs62468699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62468700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62468705	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62468707	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62468708	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62468709	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468711	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62468712	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[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	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1028692	chr7:65673136-65751069	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538908	chr7:65673136-65751069	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12531900	RABGEF1	cis	multi-tissue	Pritchard
rs12531900	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL
rs12531900	RABGEF1	cis	lymphoblastoid	seeQTL
rs12531900	hmm32897	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65701600-65729200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr7:65704200-65729200	Weak transcription	Aorta	Aorta
3	chr7:65704200-65731200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:65704400-65746800	Weak transcription	Pancreas	Pancrea
5	chr7:65705800-65729200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:65712800-65729200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:65719800-65730400	Weak transcription	Right Ventricle	heart
8	chr7:65721200-65728400	Weak transcription	Fetal Lung	lung
9	chr7:65721400-65728800	Weak transcription	NHLF	lung
10	chr7:65722200-65727000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:65723200-65728200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:65723600-65728400	Weak transcription	NHEK	skin
13	chr7:65723800-65727000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:65723800-65727200	Weak transcription	Ovary	ovary
15	chr7:65723800-65728800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:65723800-65728800	Weak transcription	Liver	Liver
17	chr7:65723800-65730200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr7:65724000-65728200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:65724000-65730400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:65724200-65727600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:65724200-65728600	Weak transcription	Osteobl	bone
22	chr7:65724200-65730000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:65724400-65727000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:65724600-65729800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:65724800-65727000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:65725000-65729200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:65725800-65727200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:65725800-65727600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr7:65726000-65728800	Weak transcription	NHDF-Ad	bronchial
30	chr7:65726200-65728400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:65726600-65727000	Weak transcription	Fetal Kidney	kidney
32	chr7:65726800-65727400	ZNF genes & repeats	HSMM	muscle
33	chr7:65726800-65727800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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