Variant report

Variant	rs4968460
Chromosome Location	chr17:59995992-59995993
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59993360..59995003-chr17:59995324..59997482,2	MCF-7	breast:
2	chr17:59994780..60000369-chr17:60000911..60007000,12	K562	blood:
3	chr17:59995985..59999406-chr17:60001386..60004929,4	K562	blood:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10512492	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes]
rs11079459	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12450560	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12451910	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12452094	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12452732	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12600620	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12600909	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12604037	0.81[CEU][hapmap];0.83[CHB][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16945692	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16945753	0.90[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16945756	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs16945759	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs16945801	0.89[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2271576	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278812	0.88[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap]
rs2378908	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs28654524	0.84[AFR][1000 genomes]
rs3744434	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809753	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs3826419	0.90[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs4422036	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs4968408	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968451	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4968452	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968454	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968455	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968456	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4968457	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4968459	0.80[ASN][1000 genomes]
rs4968461	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968462	0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4968463	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs4968464	0.96[AFR][1000 genomes]
rs4968467	0.90[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs4968468	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs4968476	0.81[CEU][hapmap]
rs4988344	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes]
rs56794817	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57137451	0.84[AFR][1000 genomes]
rs57746689	0.81[AFR][1000 genomes]
rs58085921	0.85[ASN][1000 genomes]
rs58241345	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58624595	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59080342	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60053512	0.84[AFR][1000 genomes]
rs61658218	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6504084	1.00[ASW][hapmap];0.81[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs7218724	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs7221089	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs73332565	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73332580	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73332598	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73334621	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8065778	0.90[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8066964	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8074890	0.90[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs8080599	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8081917	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9630735	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9630736	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4968460	MED13	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59941400-60004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:59941400-60004400	Weak transcription	Aorta	Aorta
3	chr17:59941400-60004400	Weak transcription	Pancreas	Pancrea
4	chr17:59941600-60003600	Weak transcription	Stomach Mucosa	stomach
5	chr17:59941600-60004400	Weak transcription	Colonic Mucosa	Colon
6	chr17:59942600-60002800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:59954400-60003800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr17:59959000-59996800	Weak transcription	Gastric	stomach
9	chr17:59959600-60003600	Weak transcription	Fetal Heart	heart
10	chr17:59966000-60004200	Weak transcription	Psoas Muscle	Psoas
11	chr17:59966200-59998000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr17:59975400-60004600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr17:59978600-60004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:59980200-60003600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:59982600-60001400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:59982600-60003600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr17:59983000-59997000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr17:59983600-60004600	Weak transcription	Spleen	Spleen
19	chr17:59984200-60003400	Weak transcription	HSMMtube	muscle
20	chr17:59985000-60004400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr17:59987800-60002600	Weak transcription	NHEK	skin
22	chr17:59989000-59996600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr17:59989000-59996800	Weak transcription	Esophagus	oesophagus
24	chr17:59989000-60001600	Weak transcription	Brain Germinal Matrix	brain
25	chr17:59989200-59996600	Weak transcription	HSMM	muscle
26	chr17:59989200-59998000	Weak transcription	Fetal Kidney	kidney
27	chr17:59989200-59998600	Weak transcription	HMEC	breast
28	chr17:59989200-60001400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr17:59989200-60003400	Weak transcription	Colon Smooth Muscle	Colon
30	chr17:59989400-59996600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr17:59989400-59996600	Weak transcription	Fetal Thymus	thymus
32	chr17:59989400-59996800	Weak transcription	Osteobl	bone
33	chr17:59989400-60001400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:59989400-60003800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr17:59989400-60003800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr17:59989400-60004400	Weak transcription	Lung	lung
37	chr17:59989600-59996800	Weak transcription	Fetal Lung	lung
38	chr17:59989600-59997000	Weak transcription	Brain Angular Gyrus	brain
39	chr17:59989600-59998200	Weak transcription	NHDF-Ad	bronchial
40	chr17:59989600-59998600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr17:59989600-60003600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr17:59989600-60003600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr17:59989600-60003600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr17:59989600-60003800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr17:59989600-60003800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr17:59989600-60003800	Weak transcription	Right Ventricle	heart
47	chr17:59989600-60003800	Weak transcription	HUVEC	blood vessel
48	chr17:59989600-60003800	Weak transcription	K562	blood
49	chr17:59989600-60003800	Weak transcription	NHLF	lung
50	chr17:59990000-59996600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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