Variant report

Variant	rs12451910
Chromosome Location	chr17:59950503-59950504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59938592..59943097-chr17:59943271..59951102,13	K562	blood:
2	chr17:59487241..59490325-chr17:59947860..59950817,3	MCF-7	breast:
3	chr17:59945351..59947710-chr17:59948808..59951151,2	K562	blood:
4	chr17:59949335..59951629-chr17:60003040..60005036,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000187013	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10512492	0.90[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs11079459	0.81[AMR][1000 genomes]
rs12450560	0.90[CEU][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs12452094	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12452732	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12600909	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12604037	0.81[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes]
rs16945692	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16945753	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs16945759	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]
rs16945801	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs2271576	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278812	0.83[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap]
rs2378908	0.83[GIH][hapmap];0.94[TSI][hapmap]
rs3744434	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3809753	0.90[CEU][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap]
rs3826419	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4422036	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]
rs4968408	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968451	1.00[CEU][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968452	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968454	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968455	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968456	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968457	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968460	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]
rs4968461	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4968462	0.82[JPT][hapmap]
rs4968463	0.85[AMR][1000 genomes]
rs4968467	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4968468	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]
rs4988344	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56794817	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58624595	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59080342	0.86[AMR][1000 genomes]
rs61169879	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61658218	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7218724	0.90[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs7221089	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]
rs73332565	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73332580	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73332598	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73334621	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8065778	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs8066964	0.90[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap]
rs8074890	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs8080599	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8081917	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9630735	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9630736	0.90[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]

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
rs12451910	MED13	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59941200-59957000	Weak transcription	Spleen	Spleen
2	chr17:59941200-59964600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:59941400-59953200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:59941400-59953200	Weak transcription	Small Intestine	intestine
5	chr17:59941400-59957000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:59941400-59957600	Weak transcription	Gastric	stomach
7	chr17:59941400-59965400	Weak transcription	Lung	lung
8	chr17:59941400-59975000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr17:59941400-60004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:59941400-60004400	Weak transcription	Aorta	Aorta
11	chr17:59941400-60004400	Weak transcription	Pancreas	Pancrea
12	chr17:59941600-59953200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr17:59941600-59957000	Weak transcription	Esophagus	oesophagus
14	chr17:59941600-59957000	Weak transcription	Thymus	Thymus
15	chr17:59941600-59965200	Weak transcription	Psoas Muscle	Psoas
16	chr17:59941600-59965400	Weak transcription	Brain Substantia Nigra	brain
17	chr17:59941600-59965600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr17:59941600-59966800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr17:59941600-59979600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr17:59941600-59987600	Weak transcription	Right Ventricle	heart
21	chr17:59941600-60003600	Weak transcription	Stomach Mucosa	stomach
22	chr17:59941600-60004400	Weak transcription	Colonic Mucosa	Colon
23	chr17:59941800-59952200	Weak transcription	Osteobl	bone
24	chr17:59941800-59953200	Weak transcription	HSMMtube	muscle
25	chr17:59941800-59954200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr17:59941800-59957000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr17:59941800-59960000	Weak transcription	NHEK	skin
28	chr17:59941800-59961000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr17:59941800-59967000	Weak transcription	Fetal Brain Male	brain
30	chr17:59941800-59968800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr17:59941800-59969200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr17:59941800-59971800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr17:59941800-59979200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr17:59941800-59979200	Weak transcription	Brain Angular Gyrus	brain
35	chr17:59942600-60002800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:59943600-59962200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:59943600-59989600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:59943800-59956800	Strong transcription	HSMM	muscle
39	chr17:59944400-59951400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr17:59944400-59962600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr17:59944400-59970000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr17:59944600-59953000	Strong transcription	Dnd41	blood
43	chr17:59944600-59955800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr17:59944600-59962600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr17:59944600-59967600	Strong transcription	HepG2	liver
46	chr17:59946200-59952200	Strong transcription	Primary T cells from cord blood	blood
47	chr17:59946600-59959600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr17:59946600-59989200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr17:59947400-59953200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr17:59947400-59954600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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