Variant report

Variant	rs7221089
Chromosome Location	chr17:60101848-60101849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60100669..60105191-chr17:60105675..60110995,6	MCF-7	breast:
2	chr17:60097595..60100490-chr17:60100782..60103714,3	K562	blood:
3	chr17:60004317..60006428-chr17:60099943..60102128,2	MCF-7	breast:
4	chr17:60099767..60102259-chr17:60130440..60133314,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction
ENSG00000108506	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10512492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450223	0.86[ASN][1000 genomes]
rs12450560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[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];0.87[TSI][hapmap]
rs12452094	1.00[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12600620	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12600909	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs12604037	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs16945692	0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs16945753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16945756	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16945759	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]
rs16945801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271576	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs2278812	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs2378908	0.88[GIH][hapmap]
rs28654524	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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];0.87[TSI][hapmap]
rs3809753	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[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];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4410139	0.85[EUR][1000 genomes]
rs4422036	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];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4968408	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs4968451	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][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];0.87[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs4968461	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4968462	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs4968463	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968464	0.81[AFR][1000 genomes];0.85[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];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968468	1.00[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];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968470	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968476	0.90[CEU][hapmap]
rs4988344	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs56794817	0.83[AMR][1000 genomes]
rs57137451	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57746689	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57918684	0.83[EUR][1000 genomes]
rs58241345	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58335059	1.00[ASN][1000 genomes]
rs59080342	0.83[AMR][1000 genomes]
rs60053512	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61469058	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61658218	0.81[AMR][1000 genomes];0.84[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];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72843781	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs73334621	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73336436	0.92[AMR][1000 genomes];0.93[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];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066964	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8080599	0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[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];0.87[TSI][hapmap]
rs9630736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	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
4	esv2753884	chr17:60077852-60190630	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv2755037	chr17:60086508-60386211	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7221089	MED13	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
3	chr17:60042800-60105200	Weak transcription	Psoas Muscle	Psoas
4	chr17:60062400-60106800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr17:60069200-60107600	Weak transcription	Spleen	Spleen
6	chr17:60074600-60123800	Weak transcription	Right Atrium	heart
7	chr17:60075800-60114400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
9	chr17:60081800-60111600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr17:60087000-60102200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr17:60088400-60107600	Weak transcription	Pancreas	Pancrea
12	chr17:60088600-60105200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr17:60088600-60105400	Weak transcription	Esophagus	oesophagus
14	chr17:60088600-60106800	Weak transcription	Fetal Heart	heart
15	chr17:60094600-60113200	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr17:60095000-60103800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr17:60095000-60112600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr17:60095000-60113200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr17:60095200-60103800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr17:60095600-60105800	Weak transcription	Brain Angular Gyrus	brain
21	chr17:60095800-60103200	Strong transcription	Fetal Intestine Small	intestine
22	chr17:60095800-60103200	Strong transcription	Fetal Stomach	stomach
23	chr17:60095800-60103800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr17:60095800-60112600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:60095800-60113000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr17:60096000-60103400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr17:60096000-60103800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:60096000-60105200	Weak transcription	NHLF	lung
29	chr17:60096000-60113000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:60096800-60105400	Weak transcription	Fetal Brain Male	brain
31	chr17:60097000-60102800	Weak transcription	NHEK	skin
32	chr17:60097000-60113000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr17:60097000-60113000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr17:60098600-60102400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr17:60098600-60104000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr17:60098600-60111400	Strong transcription	Fetal Lung	lung
37	chr17:60098600-60112400	Strong transcription	Fetal Muscle Leg	muscle
38	chr17:60098600-60114600	Strong transcription	Placenta	Placenta
39	chr17:60098600-60139200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr17:60098800-60102400	Strong transcription	Gastric	stomach
41	chr17:60098800-60103200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr17:60098800-60103200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:60098800-60103400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr17:60098800-60103600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr17:60098800-60104600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr17:60098800-60107600	Strong transcription	Liver	Liver
47	chr17:60098800-60111000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr17:60098800-60111600	Strong transcription	Thymus	Thymus
49	chr17:60098800-60112600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr17:60098800-60112800	Strong transcription	H1 Cell Line	embryonic stem cell

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