Variant report

Variant	rs12538379
Chromosome Location	chr7:65770639-65770640
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	chr7:65669909..65672272-chr7:65770013..65772030,2	MCF-7	breast:
2	chr7:65765329..65768039-chr7:65770464..65772414,2	K562	blood:

Variant related genes	Relation type
ENSG00000169902	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs12530506	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12530746	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12530898	1.00[AFR][1000 genomes]
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[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]
rs12532060	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532173	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532182	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532247	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532249	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532278	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532327	1.00[AFR][1000 genomes]
rs12532383	1.00[EUR][1000 genomes]
rs12532423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12532657	0.97[EUR][1000 genomes];0.84[ASN][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[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]
rs12533387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12533877	1.00[EUR][1000 genomes]
rs12534039	0.97[EUR][1000 genomes];0.84[ASN][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[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12534249	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12534263	0.97[EUR][1000 genomes]
rs12534477	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12534881	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12535985	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12536816	0.89[EUR][1000 genomes]
rs12536818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12537039	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12537368	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12537698	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537936	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12538011	0.97[EUR][1000 genomes]
rs12538025	1.00[AFR][1000 genomes]
rs12538113	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12538147	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12538686	0.92[EUR][1000 genomes]
rs12538961	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539795	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12540667	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12540888	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[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];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[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];0.89[EUR][1000 genomes]
rs35910256	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3735145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3735146	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[EUR][1000 genomes]
rs3735150	1.00[EUR][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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[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];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4717291	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4718342	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718345	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718347	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718350	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718353	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718354	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465362	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465363	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465364	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465365	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465367	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465372	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62465373	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62465376	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465377	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465380	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62465389	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465390	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465391	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465392	1.00[EUR][1000 genomes]
rs62465394	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465395	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465396	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465397	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465399	0.92[EUR][1000 genomes]
rs62465400	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465401	1.00[EUR][1000 genomes]
rs62465402	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465403	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465404	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465405	0.92[EUR][1000 genomes]
rs62465422	1.00[EUR][1000 genomes]
rs62465424	1.00[EUR][1000 genomes]
rs62465425	1.00[EUR][1000 genomes]
rs62465426	0.97[EUR][1000 genomes]
rs62465427	0.81[EUR][1000 genomes]
rs62465428	1.00[EUR][1000 genomes]
rs62465429	1.00[EUR][1000 genomes]
rs62465431	1.00[EUR][1000 genomes]
rs62465432	0.97[EUR][1000 genomes]
rs62465433	0.95[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];0.82[EUR][1000 genomes]
rs62465484	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465512	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465513	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465515	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465519	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465521	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465522	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465525	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465526	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465527	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62465542	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62465545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62465546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62465547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62465550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62465552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62465554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][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];1.00[ASN][1000 genomes]
rs62468677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62468679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62468696	1.00[EUR][1000 genomes]
rs62468699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62468700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62468702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62468705	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468707	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62468708	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62468709	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62468711	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468712	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][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	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
4	nsv1034195	chr7:65743409-65828266	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats 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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12538379	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL
rs12538379	RABGEF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65761600-65772400	Weak transcription	HSMM	muscle
2	chr7:65763000-65786200	Weak transcription	Primary B cells from cord blood	blood
3	chr7:65766400-65777600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:65766800-65780200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:65767800-65772600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:65768000-65780200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:65768200-65771600	Enhancers	NHEK	skin
8	chr7:65768200-65773000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr7:65768200-65773400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:65768200-65780200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:65768600-65771800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:65768800-65771600	Enhancers	Fetal Kidney	kidney
13	chr7:65768800-65773600	Enhancers	Stomach Mucosa	stomach
14	chr7:65769000-65772800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:65769200-65770800	Enhancers	Spleen	Spleen
16	chr7:65769200-65772400	Weak transcription	Fetal Intestine Large	intestine
17	chr7:65769400-65771000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:65769400-65772600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:65769400-65776200	Weak transcription	Lung	lung
20	chr7:65769400-65779600	Weak transcription	Fetal Stomach	stomach
21	chr7:65769600-65772400	Weak transcription	NHDF-Ad	bronchial
22	chr7:65769600-65772400	Weak transcription	NHLF	lung
23	chr7:65769600-65772600	Weak transcription	Esophagus	oesophagus
24	chr7:65769600-65772600	Weak transcription	Gastric	stomach
25	chr7:65769600-65772600	Weak transcription	Right Atrium	heart
26	chr7:65769600-65774400	Weak transcription	Colon Smooth Muscle	Colon
27	chr7:65769800-65770800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:65769800-65770800	Weak transcription	HMEC	breast
29	chr7:65769800-65771000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:65769800-65771000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr7:65769800-65771000	Weak transcription	Fetal Lung	lung
32	chr7:65769800-65772600	Weak transcription	NH-A	brain
33	chr7:65769800-65774800	Enhancers	HUVEC	blood vessel
34	chr7:65770000-65771000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:65770000-65771000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:65770000-65771200	Weak transcription	Pancreas	Pancrea
37	chr7:65770000-65771200	Weak transcription	Osteobl	bone
38	chr7:65770000-65772400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr7:65770000-65772600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:65770000-65772600	Weak transcription	Left Ventricle	heart
41	chr7:65770200-65771200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr7:65770200-65772600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:65770400-65775600	Enhancers	HepG2	liver
44	chr7:65770600-65771800	Enhancers	Ovary	ovary

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