Variant report

Variant	rs7784623
Chromosome Location	chr7:65395034-65395035
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65389752..65391317-chr7:65393803..65395950,2	MCF-7	breast:
2	chr7:65391429..65394258-chr7:65394498..65396137,2	K562	blood:
3	chr7:65391954..65395271-chr7:65397113..65402077,6	K562	blood:
4	chr7:65391913..65395079-chr7:65403805..65405428,3	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10229450	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10279841	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10807697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1167385	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1167386	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11763147	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap]
rs11768292	0.88[ASN][1000 genomes]
rs11770828	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs12670952	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12698512	0.86[ASN][1000 genomes]
rs13237956	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1631091	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1701751	0.86[EUR][1000 genomes]
rs1701757	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1701760	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1723268	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1723275	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1829943	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs1880556	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1917563	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2008188	0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2462573	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2658585	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2658587	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2690442	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs2692056	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2939548	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2946579	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2949690	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2949692	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3201569	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34973832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35135885	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35850374	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4467826	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718288	0.84[EUR][1000 genomes]
rs55773927	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55796207	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56028712	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62470893	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66552782	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6945322	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6946143	0.86[ASW][hapmap]
rs6954920	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6955582	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6960048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6961717	0.87[ASW][hapmap]
rs709604	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs736270	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7383796	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7791814	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7809991	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs781143	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs781144	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs781145	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs781151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs781152	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9530	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[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	nsv429767	chr7:64473713-65415647	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1020337	chr7:65371505-65449654	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs7784623	RABGEF1	cis	cerebellum	SCAN
rs7784623	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs7784623	CRCP	cis	parietal	SCAN
rs7784623	ERV3	cis	cerebellum	SCAN
rs7784623	KCTD7	cis	parietal	SCAN
rs7784623	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7784623	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs7784623	GUSB	cis	parietal	SCAN
rs7784623	GUSB	cis	cerebellum	SCAN
rs7784623	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs7784623	NCRNA00174	cis	cerebellum	SCAN
rs7784623	GUSB	cis	lymphoblastoid	seeQTL
rs7784623	RP4-756H11.3	cis	lung	GTEx
rs7784623	ERV3	cis	parietal	SCAN
rs7784623	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs7784623	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs7784623	RP4-756H11.3	cis	Artery Tibial	GTEx
rs7784623	CRCP	cis	cerebellum	SCAN
rs7784623	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs7784623	RP4-756H11.3	cis	Thyroid	GTEx
rs7784623	ZNF273	cis	cerebellum	SCAN
rs7784623	RP4-756H11.3	cis	Artery Aorta	GTEx
rs7784623	RP4-756H11.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65345200-65419000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr7:65366400-65406800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:65366800-65403600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:65368800-65403600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:65368800-65418800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:65368800-65419000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:65369600-65403600	Weak transcription	Fetal Stomach	stomach
8	chr7:65369600-65405800	Weak transcription	NHEK	skin
9	chr7:65373000-65403200	Weak transcription	A549	lung
10	chr7:65373800-65424000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:65374800-65402800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:65375000-65418800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:65375400-65396600	Weak transcription	Liver	Liver
14	chr7:65375600-65419800	Weak transcription	HSMMtube	muscle
15	chr7:65377600-65402600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:65379200-65419000	Weak transcription	Fetal Thymus	thymus
17	chr7:65381800-65420200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr7:65382000-65420600	Weak transcription	Primary B cells from cord blood	blood
19	chr7:65382800-65419800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:65383200-65419000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:65383800-65419600	Weak transcription	GM12878-XiMat	blood
22	chr7:65384000-65405600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:65384400-65401800	Weak transcription	Dnd41	blood
24	chr7:65385200-65401800	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:65385600-65396800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:65389400-65396600	Weak transcription	Psoas Muscle	Psoas
27	chr7:65389400-65406000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr7:65389400-65423800	Weak transcription	Aorta	Aorta
29	chr7:65390400-65403800	Weak transcription	Adipose Nuclei	Adipose
30	chr7:65390400-65419000	Weak transcription	Thymus	Thymus
31	chr7:65390600-65423800	Weak transcription	Gastric	stomach
32	chr7:65390800-65395200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:65390800-65401600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr7:65392600-65418400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:65392800-65396800	Weak transcription	Lung	lung
36	chr7:65392800-65396800	Weak transcription	HepG2	liver
37	chr7:65392800-65397000	Weak transcription	Left Ventricle	heart
38	chr7:65392800-65402200	Weak transcription	Primary T cells from cord blood	blood
39	chr7:65392800-65412600	Weak transcription	Pancreas	Pancrea
40	chr7:65393000-65401400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:65393000-65411800	Weak transcription	Ovary	ovary
42	chr7:65393200-65419600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr7:65393400-65401400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr7:65393400-65419000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:65393800-65395400	Weak transcription	Fetal Lung	lung
46	chr7:65393800-65400200	Weak transcription	Fetal Intestine Small	intestine
47	chr7:65393800-65403600	Weak transcription	Fetal Intestine Large	intestine
48	chr7:65394000-65395600	Enhancers	K562	blood
49	chr7:65394000-65403200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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