Variant report

Variant	rs10950029
Chromosome Location	chr7:65634321-65634322
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65630028..65632424-chr7:65633980..65636859,2	K562	blood:
2	chr7:65633079..65635754-chr7:65815405..65818400,2	K562	blood:

Variant related genes	Relation type
ENSG00000169902	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10447522	0.82[YRI][hapmap]
rs10950024	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10950025	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10950026	1.00[CEU][hapmap]
rs10950027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10950028	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11760805	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11767262	0.81[EUR][1000 genomes]
rs11767833	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11769702	0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs12666485	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12671834	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12673308	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1547529	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs160641	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs160645	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs160647	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17138089	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17138149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17138156	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1909508	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2088655	0.82[YRI][hapmap]
rs221986	0.87[ASN][1000 genomes]
rs2420456	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2451953	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2460427	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465121	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28815324	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2946580	0.83[AMR][1000 genomes]
rs313817	0.90[ASN][1000 genomes]
rs313818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs313823	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs313828	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs313829	0.87[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]
rs313830	1.00[ASW][hapmap];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs316305	0.86[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];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316306	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316316	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs316320	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316323	0.86[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];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs316324	0.86[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];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs316328	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs400767	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4441996	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4718325	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6460276	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460281	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66594357	0.81[EUR][1000 genomes]
rs67302640	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67397473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67688847	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67775320	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6960870	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6979636	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs73136346	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73142233	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73142245	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73142265	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73376394	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73376401	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73378304	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7782212	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7783727	0.84[ASN][1000 genomes]
rs7783889	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7786728	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7786735	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7787063	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778736	0.82[YRI][hapmap]

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	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
2	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
3	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv971172	chr7:65616238-65653268	Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs10950029	RABGEF1	cis	cerebellum	SCAN
rs10950029	GS1-124K5.11	cis	Thyroid	GTEx
rs10950029	ERV3	cis	multi-tissue	Pritchard
rs10950029	ZNF273	cis	cerebellum	SCAN
rs10950029	VKORC1L1	cis	multi-tissue	Pritchard
rs10950029	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs10950029	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs10950029	RABGEF1	cis	parietal	SCAN
rs10950029	GS1-124K5.4	cis	Artery Aorta	GTEx
rs10950029	RNU6-96P	cis	Thyroid	GTEx
rs10950029	GUSB	cis	parietal	SCAN
rs10950029	GTF2IRD1P1	cis	Thyroid	GTEx
rs10950029	ZNF92	cis	parietal	SCAN
rs10950029	GS1-124K5.4	cis	Stomach	GTEx
rs10950029	TPST1	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65612000-65635400	Weak transcription	Fetal Kidney	kidney
2	chr7:65618200-65635400	Weak transcription	Esophagus	oesophagus
3	chr7:65618200-65635600	Weak transcription	Right Ventricle	heart
4	chr7:65619000-65635200	Weak transcription	Spleen	Spleen
5	chr7:65619000-65635400	Weak transcription	Pancreas	Pancrea
6	chr7:65619000-65635600	Weak transcription	HMEC	breast
7	chr7:65619000-65635800	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:65620800-65635400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr7:65622600-65635600	Weak transcription	Stomach Mucosa	stomach
10	chr7:65623600-65635400	Weak transcription	Colonic Mucosa	Colon
11	chr7:65623600-65635600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:65623800-65635400	Weak transcription	Adipose Nuclei	Adipose
13	chr7:65623800-65635400	Weak transcription	Lung	lung
14	chr7:65623800-65635400	Weak transcription	Ovary	ovary
15	chr7:65623800-65635400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:65623800-65635400	Weak transcription	HSMMtube	muscle
17	chr7:65624000-65634800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:65624000-65634800	Weak transcription	Left Ventricle	heart
19	chr7:65624400-65635200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:65624400-65635400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:65624600-65635600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:65625800-65635400	Weak transcription	Fetal Muscle Leg	muscle
23	chr7:65626400-65637600	Weak transcription	Fetal Brain Female	brain
24	chr7:65633000-65635400	Weak transcription	Fetal Stomach	stomach
25	chr7:65633000-65635400	Weak transcription	Right Atrium	heart
26	chr7:65633000-65635400	Weak transcription	NHDF-Ad	bronchial
27	chr7:65633200-65634600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:65633200-65635200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr7:65633200-65635400	Weak transcription	Fetal Lung	lung
30	chr7:65633200-65635400	Weak transcription	NHLF	lung
31	chr7:65633200-65635600	Weak transcription	Gastric	stomach
32	chr7:65633400-65634600	Weak transcription	A549	lung
33	chr7:65633400-65634800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:65633400-65634800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:65633400-65635000	Weak transcription	HepG2	liver
36	chr7:65633400-65635400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:65633400-65635400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr7:65633400-65635400	Weak transcription	Brain Germinal Matrix	brain
39	chr7:65633400-65635400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr7:65633400-65635400	Weak transcription	Hela-S3	cervix
41	chr7:65633400-65635400	Weak transcription	K562	blood
42	chr7:65633400-65635400	Weak transcription	Osteobl	bone
43	chr7:65633400-65635600	Weak transcription	NH-A	brain
44	chr7:65633800-65635400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:65634000-65635400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:65634200-65635400	Weak transcription	Fetal Brain Male	brain

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