Variant report

Variant	rs1962050
Chromosome Location	chr7:66240008-66240009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66233619..66236445-chr7:66238794..66241787,2	MCF-7	breast:
2	chr7:66203830..66206564-chr7:66239736..66241863,2	K562	blood:
3	chr7:66232638..66234742-chr7:66239785..66241846,2	K562	blood:

Variant related genes	Relation type
ENSG00000154710	Chromatin interaction
ENSG00000243335	Chromatin interaction
ENSG00000272831	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1016265	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10233806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10244498	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10252765	0.86[MKK][hapmap]
rs10278014	0.88[CEU][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap];0.86[LWK][hapmap];0.91[TSI][hapmap]
rs10281499	0.82[CHB][hapmap]
rs10950049	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10950050	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11761542	0.88[CEU][hapmap]
rs11772819	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13226966	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13308803	0.87[CEU][hapmap];0.85[CHB][hapmap];0.88[YRI][hapmap]
rs1544549	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1860469	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs2003300	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2013908	0.89[CEU][hapmap]
rs2109297	0.89[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.86[LWK][hapmap];0.91[TSI][hapmap]
rs2191268	0.86[MKK][hapmap]
rs2420820	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2659892	0.83[CEU][hapmap]
rs2659893	0.88[CEU][hapmap];0.83[CHB][hapmap]
rs2659894	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2659895	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659897	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2659900	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2659904	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2659914	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2707824	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs2707839	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2707854	0.88[MKK][hapmap]
rs2707856	0.88[MKK][hapmap]
rs3764903	0.86[MKK][hapmap]
rs3846973	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.85[LWK][hapmap];0.91[TSI][hapmap]
rs3857687	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4610622	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718383	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs4718428	0.81[MKK][hapmap]
rs6460305	0.88[MKK][hapmap]
rs6460307	0.89[CEU][hapmap];0.83[GIH][hapmap];0.86[LWK][hapmap];0.91[TSI][hapmap]
rs6951302	0.86[CEU][hapmap];0.80[CHB][hapmap];0.86[YRI][hapmap]
rs6955837	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs6958200	0.86[EUR][1000 genomes]
rs6958520	0.88[MKK][hapmap]
rs6969679	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7800620	0.86[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs974239	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9791713	0.89[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.85[LWK][hapmap];0.88[TSI][hapmap]

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
rs1962050	RP4-756H11.3	cis	lung	GTEx
rs1962050	GUSB	cis	parietal	SCAN
rs1962050	RP4-756H11.3	cis	Thyroid	GTEx
rs1962050	GUSB	cis	cerebellum	SCAN
rs1962050	RP4-756H11.3	cis	Artery Tibial	GTEx
rs1962050	GS1-124K5.4	cis	Artery Aorta	GTEx
rs1962050	CRCP	cis	parietal	SCAN
rs1962050	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs1962050	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs1962050	SBDS	cis	cerebellum	SCAN
rs1962050	CRCP	cis	cerebellum	SCAN
rs1962050	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs1962050	GS1-124K5.4	cis	Stomach	GTEx
rs1962050	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1962050	RABGEF1	cis	cerebellum	SCAN
rs1962050	GS1-124K5.4	cis	Esophagus Muscularis	GTEx
rs1962050	VKORC1L1	cis	multi-tissue	Pritchard
rs1962050	RP4-756H11.3	cis	Artery Aorta	GTEx
rs1962050	TPST1	cis	lymphoblastoid	seeQTL
rs1962050	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs1962050	TPST1	cis	multi-tissue	Pritchard
rs1962050	GTF2IRD1P1	cis	Thyroid	GTEx
rs1962050	RNU6-96P	cis	Thyroid	GTEx
rs1962050	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs1962050	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs1962050	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs1962050	GS1-124K5.11	cis	Thyroid	GTEx
rs1962050	LOC285908	cis	multi-tissue	Pritchard

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	chr7:66208000-66240800	Weak transcription	HSMMtube	muscle
3	chr7:66208000-66241800	Weak transcription	Hela-S3	cervix
4	chr7:66220000-66241000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:66221800-66240400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:66227000-66243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:66231200-66246400	Weak transcription	Right Ventricle	heart
8	chr7:66231400-66255000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:66233000-66241600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr7:66234200-66241800	Weak transcription	Small Intestine	intestine
12	chr7:66234800-66243600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:66234800-66275800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:66235000-66240400	Weak transcription	K562	blood
15	chr7:66235200-66261400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:66235400-66241000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:66235400-66255400	Weak transcription	Fetal Heart	heart
18	chr7:66236000-66259000	Strong transcription	NHDF-Ad	bronchial
19	chr7:66236600-66241000	Strong transcription	Fetal Intestine Small	intestine
20	chr7:66236600-66244600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:66236800-66242400	Strong transcription	HSMM	muscle
22	chr7:66236800-66242800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:66236800-66243400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:66236800-66243800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:66236800-66244800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr7:66236800-66245400	Strong transcription	GM12878-XiMat	blood
27	chr7:66236800-66247800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:66236800-66265200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr7:66236800-66276800	Strong transcription	Dnd41	blood
30	chr7:66236800-66277000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr7:66236800-66278400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:66237000-66243800	Strong transcription	Fetal Thymus	thymus
33	chr7:66237000-66244800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:66237000-66245000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr7:66237000-66245400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:66237200-66244000	Strong transcription	Placenta	Placenta
37	chr7:66237200-66262400	Weak transcription	Fetal Brain Male	brain
38	chr7:66237200-66277600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:66237400-66242000	Strong transcription	Fetal Stomach	stomach
40	chr7:66238000-66242200	Strong transcription	Spleen	Spleen
41	chr7:66238000-66243600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr7:66238000-66246600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr7:66238000-66253800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr7:66238200-66240400	Strong transcription	Psoas Muscle	Psoas
45	chr7:66238200-66241000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr7:66238200-66241800	Strong transcription	Fetal Intestine Large	intestine
47	chr7:66238200-66242200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:66238200-66242200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr7:66238200-66242200	Strong transcription	Esophagus	oesophagus
50	chr7:66238200-66244600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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