Variant report

Variant	rs16945759
Chromosome Location	chr17:60075148-60075149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60073399..60075820-chr17:60081958..60084640,4	K562	blood:
2	chr17:60073745..60080037-chr17:60141908..60144037,6	MCF-7	breast:
3	chr17:60065234..60067787-chr17:60072836..60076599,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction
ENSG00000242398	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10512492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11079459	0.84[AFR][1000 genomes]
rs12450223	0.84[ASN][1000 genomes]
rs12450560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12451910	0.90[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap]
rs12452094	1.00[CEU][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12452732	0.83[AMR][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs12600620	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12600909	0.90[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs12604037	0.90[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16945692	0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs16945753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16945756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16945801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271576	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs2278812	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[ASN][1000 genomes]
rs2378908	0.88[GIH][hapmap];0.88[TSI][hapmap]
rs28654524	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3744434	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes]
rs3809753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3826419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4410139	0.84[EUR][1000 genomes]
rs4422036	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs4968408	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs4968451	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap]
rs4968455	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4968456	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4968457	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs4968460	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]
rs4968461	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4968462	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4968463	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968464	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4968467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968468	1.00[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];0.82[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968470	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968476	0.90[CEU][hapmap]
rs4988344	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs56794817	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57137451	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57746689	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58241345	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58335059	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58624595	0.83[AMR][1000 genomes]
rs59080342	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60053512	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61469058	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61658218	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6504084	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap]
rs7218724	1.00[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];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7221089	1.00[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];0.82[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72843781	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs73332598	0.83[AMR][1000 genomes]
rs73334621	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73336436	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8065778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8066964	1.00[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];0.82[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8074890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8080599	0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap]
rs8081917	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes]
rs9630736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1062816	chr17:60074670-60470465	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16945759	MED13	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60021200-60097000	Strong transcription	Dnd41	blood
2	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
4	chr17:60042800-60105200	Weak transcription	Psoas Muscle	Psoas
5	chr17:60048800-60097600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr17:60050200-60100800	Weak transcription	Small Intestine	intestine
7	chr17:60059000-60088000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:60059800-60075200	Weak transcription	Fetal Heart	heart
9	chr17:60060400-60081800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:60060400-60086800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr17:60060400-60088000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:60060400-60090600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr17:60060400-60096200	Weak transcription	Fetal Brain Male	brain
14	chr17:60060400-60098800	Weak transcription	Gastric	stomach
15	chr17:60060400-60099800	Weak transcription	Aorta	Aorta
16	chr17:60061600-60099600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr17:60062400-60081600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr17:60062400-60086400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr17:60062400-60106800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr17:60064800-60088200	Weak transcription	Pancreas	Pancrea
21	chr17:60067400-60081600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr17:60067800-60086400	Weak transcription	HMEC	breast
23	chr17:60068400-60081600	Weak transcription	Fetal Kidney	kidney
24	chr17:60069200-60107600	Weak transcription	Spleen	Spleen
25	chr17:60069400-60082600	Weak transcription	Brain Germinal Matrix	brain
26	chr17:60069400-60087000	Weak transcription	Left Ventricle	heart
27	chr17:60069600-60077000	Weak transcription	Ovary	ovary
28	chr17:60069600-60081600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr17:60069600-60099000	Weak transcription	Colonic Mucosa	Colon
30	chr17:60069800-60087800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr17:60070000-60075600	Weak transcription	NHLF	lung
32	chr17:60070000-60077600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr17:60070000-60081400	Weak transcription	Hela-S3	cervix
34	chr17:60070200-60075600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr17:60070200-60076400	Weak transcription	K562	blood
36	chr17:60070200-60088000	Weak transcription	NHEK	skin
37	chr17:60070600-60075600	Weak transcription	Brain Hippocampus Middle	brain
38	chr17:60070800-60077200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr17:60070800-60086400	Weak transcription	Fetal Brain Female	brain
40	chr17:60071000-60083200	Weak transcription	Esophagus	oesophagus
41	chr17:60071400-60075800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr17:60071600-60082800	Weak transcription	Lung	lung
43	chr17:60071800-60075600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:60071800-60082000	Weak transcription	Thymus	Thymus
45	chr17:60071800-60082200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:60072000-60077200	Weak transcription	GM12878-XiMat	blood
47	chr17:60072200-60081800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr17:60072200-60087800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr17:60072400-60076000	Weak transcription	Fetal Intestine Small	intestine
50	chr17:60072400-60081800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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