Variant report

Variant	rs10950050
Chromosome Location	chr7:66239588-66239589
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	chr7:66233619..66236445-chr7:66238794..66241787,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1016265	0.81[AMR][1000 genomes]
rs10233806	0.89[CEU][hapmap];0.83[CHB][hapmap];0.88[YRI][hapmap]
rs10244498	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap]
rs10274883	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10278014	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[EUR][1000 genomes]
rs10281499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs10950046	0.86[EUR][1000 genomes]
rs10950049	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11761542	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11772819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12333370	0.90[EUR][1000 genomes]
rs13226966	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13240501	0.84[EUR][1000 genomes]
rs13242290	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13308803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1860469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1860472	0.90[EUR][1000 genomes]
rs1962050	0.89[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1968126	0.83[EUR][1000 genomes]
rs2003300	0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs2013908	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2024192	0.86[EUR][1000 genomes]
rs2109297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2244022	0.83[MKK][hapmap]
rs2659890	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2659891	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659892	0.95[CEU][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659894	0.81[AFR][1000 genomes]
rs2659895	0.81[AFR][1000 genomes]
rs2659896	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2659897	0.81[AFR][1000 genomes]
rs2659898	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2659901	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2659907	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2659908	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2707824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2707837	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2707839	0.81[AFR][1000 genomes]
rs2707847	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28431318	0.81[EUR][1000 genomes]
rs28480509	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28731376	0.82[EUR][1000 genomes]
rs3778909	0.89[YRI][hapmap]
rs3846973	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3926380	0.90[EUR][1000 genomes]
rs4506088	0.89[EUR][1000 genomes]
rs4610622	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4717315	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4718377	0.87[EUR][1000 genomes]
rs4718383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58347342	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6460307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs66981195	0.89[EUR][1000 genomes]
rs6951302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6951946	0.86[EUR][1000 genomes]
rs6955837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[EUR][1000 genomes]
rs6971059	0.87[EUR][1000 genomes]
rs6975044	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6978178	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs721717	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7384021	0.89[EUR][1000 genomes]
rs7385102	0.83[EUR][1000 genomes]
rs7782587	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7793723	0.81[EUR][1000 genomes]
rs7800620	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7805152	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7808013	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs801194	0.86[EUR][1000 genomes]
rs801195	0.85[EUR][1000 genomes]
rs881285	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs974239	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.84[LWK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs9791712	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9791713	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[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	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
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv981512	chr7:66223352-66249901	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:28)

SNP	Gene	Cis/trans	Tissue	Source
rs10950050	GTF2IRD1P1	cis	Thyroid	GTEx
rs10950050	GS1-124K5.4	cis	Artery Aorta	GTEx
rs10950050	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs10950050	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs10950050	RP4-756H11.3	cis	lung	GTEx
rs10950050	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs10950050	RNU6-96P	cis	Thyroid	GTEx
rs10950050	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs10950050	GUSB	cis	cerebellum	SCAN
rs10950050	VKORC1L1	cis	multi-tissue	Pritchard
rs10950050	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs10950050	GS1-124K5.11	cis	Thyroid	GTEx
rs10950050	RP4-756H11.3	cis	Thyroid	GTEx
rs10950050	LINC00174	cis	Thyroid	GTEx
rs10950050	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs10950050	RABGEF1	cis	cerebellum	SCAN
rs10950050	TPST1	cis	multi-tissue	Pritchard
rs10950050	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs10950050	RP4-756H11.3	cis	Artery Aorta	GTEx
rs10950050	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs10950050	ZNF273	cis	cerebellum	SCAN
rs10950050	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs10950050	TPST1	cis	lymphoblastoid	seeQTL
rs10950050	RP4-756H11.3	cis	Artery Tibial	GTEx
rs10950050	GS1-124K5.4	cis	Stomach	GTEx
rs10950050	RP4-756H11.3	cis	Whole Blood	GTEx
rs10950050	GUSB	cis	parietal	SCAN
rs10950050	GS1-124K5.2	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66207000-66255200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:66207600-66239800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:66208000-66240800	Weak transcription	HSMMtube	muscle
4	chr7:66208000-66241800	Weak transcription	Hela-S3	cervix
5	chr7:66220000-66241000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:66221800-66240400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:66227000-66243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:66231200-66246400	Weak transcription	Right Ventricle	heart
9	chr7:66231400-66255000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:66233000-66241600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:66233200-66239600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr7:66234200-66241800	Weak transcription	Small Intestine	intestine
14	chr7:66234800-66243600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:66234800-66275800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr7:66235000-66240400	Weak transcription	K562	blood
17	chr7:66235200-66261400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:66235400-66239600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:66235400-66239600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr7:66235400-66241000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:66235400-66255400	Weak transcription	Fetal Heart	heart
22	chr7:66235800-66239600	Weak transcription	Colonic Mucosa	Colon
23	chr7:66236000-66259000	Strong transcription	NHDF-Ad	bronchial
24	chr7:66236600-66241000	Strong transcription	Fetal Intestine Small	intestine
25	chr7:66236600-66244600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:66236800-66242400	Strong transcription	HSMM	muscle
27	chr7:66236800-66242800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:66236800-66243400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:66236800-66243800	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr7:66236800-66244800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:66236800-66245400	Strong transcription	GM12878-XiMat	blood
32	chr7:66236800-66247800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr7:66236800-66265200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr7:66236800-66276800	Strong transcription	Dnd41	blood
35	chr7:66236800-66277000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr7:66236800-66278400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:66237000-66239600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr7:66237000-66243800	Strong transcription	Fetal Thymus	thymus
39	chr7:66237000-66244800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:66237000-66245000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr7:66237000-66245400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:66237200-66244000	Strong transcription	Placenta	Placenta
43	chr7:66237200-66262400	Weak transcription	Fetal Brain Male	brain
44	chr7:66237200-66277600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:66237400-66242000	Strong transcription	Fetal Stomach	stomach
46	chr7:66238000-66242200	Strong transcription	Spleen	Spleen
47	chr7:66238000-66243600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr7:66238000-66246600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr7:66238000-66253800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr7:66238200-66240400	Strong transcription	Psoas Muscle	Psoas

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