Variant report

Variant	rs12532675
Chromosome Location	chr7:65706814-65706815
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	chr7:65705536..65707290-chr7:65707942..65710882,2	K562	blood:

Extended variants
information (count: 118 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs12530506	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[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]
rs12531900	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]
rs12532060	0.87[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];0.86[ASN][1000 genomes]
rs12532657	0.87[EUR][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]
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];0.84[ASN][1000 genomes]
rs12537936	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12538025	1.00[AFR][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];0.89[ASN][1000 genomes]
rs12538961	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][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];0.84[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]
rs3735145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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]
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];0.84[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]
rs62465363	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62465364	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62465365	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62465367	0.87[AMR][1000 genomes];0.87[EUR][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]
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];0.84[ASN][1000 genomes]
rs62465547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62465554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62467385	1.00[AFR][1000 genomes]
rs62467386	1.00[AFR][1000 genomes]
rs62467410	1.00[AFR][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];0.95[ASN][1000 genomes]
rs62468673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62468674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62468677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[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];0.82[ASN][1000 genomes]
rs62468700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62468702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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]
rs62468708	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62468709	0.81[EUR][1000 genomes]
rs62468711	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62468712	0.87[AMR][1000 genomes];0.84[EUR][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12532675	RABGEF1	cis	lymphoblastoid	seeQTL
rs12532675	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL
rs12532675	hmm32897	cis	multi-tissue	Pritchard
rs12532675	RABGEF1	cis	multi-tissue	Pritchard
rs12532675	LOC285908	cis	multi-tissue	Pritchard

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65672200-65723400	Weak transcription	Right Atrium	heart
2	chr7:65676000-65716800	Weak transcription	Primary B cells from cord blood	blood
3	chr7:65686800-65715400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr7:65689600-65715800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr7:65695800-65709400	Weak transcription	Psoas Muscle	Psoas
6	chr7:65699000-65712400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:65701600-65729200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:65702200-65711200	Weak transcription	Brain Anterior Caudate	brain
9	chr7:65702400-65723600	Weak transcription	Gastric	stomach
10	chr7:65703000-65715800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr7:65703800-65716600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:65704000-65712800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr7:65704000-65726800	Weak transcription	HSMM	muscle
14	chr7:65704200-65707000	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:65704200-65709600	Weak transcription	A549	lung
16	chr7:65704200-65711400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr7:65704200-65711600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:65704200-65715200	Weak transcription	Fetal Muscle Leg	muscle
19	chr7:65704200-65729200	Weak transcription	Aorta	Aorta
20	chr7:65704200-65731200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:65704400-65709400	Weak transcription	Stomach Mucosa	stomach
22	chr7:65704400-65710200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:65704400-65720200	Weak transcription	HSMMtube	muscle
24	chr7:65704400-65721800	Weak transcription	Fetal Intestine Small	intestine
25	chr7:65704400-65746800	Weak transcription	Pancreas	Pancrea
26	chr7:65704600-65709000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:65704600-65709600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr7:65704600-65710400	Weak transcription	Fetal Lung	lung
29	chr7:65704600-65716200	Weak transcription	Fetal Intestine Large	intestine
30	chr7:65704800-65720200	Weak transcription	NHLF	lung
31	chr7:65705200-65708400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:65705200-65709600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:65705400-65707000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:65705400-65707200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:65705400-65707200	Strong transcription	Liver	Liver
36	chr7:65705400-65707600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:65705600-65707000	Strong transcription	Fetal Kidney	kidney
38	chr7:65705800-65707800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:65705800-65709000	Weak transcription	Ovary	ovary
40	chr7:65705800-65711200	Weak transcription	Lung	lung
41	chr7:65705800-65712400	Weak transcription	HMEC	breast
42	chr7:65705800-65716400	Weak transcription	Esophagus	oesophagus
43	chr7:65705800-65729200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr7:65706000-65711000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:65706000-65712000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:65706000-65712200	Weak transcription	HepG2	liver
47	chr7:65706000-65716800	Weak transcription	Fetal Stomach	stomach
48	chr7:65706000-65720200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:65706200-65712200	Weak transcription	Left Ventricle	heart
50	chr7:65706200-65715200	Weak transcription	NHEK	skin

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