Variant report

Variant	rs17158453
Chromosome Location	chr11:63396384-63396385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63389927..63391632-chr11:63394971..63396472,2	K562	blood:
2	chr11:62647557..62650235-chr11:63396327..63397998,2	MCF-7	breast:
3	chr11:63389782..63392206-chr11:63395885..63397401,2	MCF-7	breast:
4	chr11:63326180..63328282-chr11:63394153..63397147,2	MCF-7	breast:
5	chr11:63379925..63381786-chr11:63395666..63398629,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176485	Chromatin interaction
ENSG00000168003	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10501394	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231535	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231543	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231545	1.00[CEU][hapmap]
rs11551942	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11551944	0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11820129	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186941	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211688	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12274980	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656941	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789219	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2509744	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959876	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959880	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959881	0.88[EUR][1000 genomes]
rs2959886	0.86[EUR][1000 genomes]
rs3016865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34109368	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35345497	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754698	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476034	1.00[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476691	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482915	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484619	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491231	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500726	0.91[EUR][1000 genomes]
rs500991	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511819	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515645	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517700	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518490	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518692	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521464	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523093	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523809	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534505	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534876	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539306	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541809	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs550629	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557882	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559405	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs560938	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562549	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566813	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567756	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568769	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568790	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580695	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588523	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928162	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928163	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928165	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928166	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928167	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928168	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928195	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928196	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928197	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928202	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928203	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928204	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928205	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928206	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928208	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928209	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928211	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928212	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928214	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928234	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928236	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928237	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928238	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928239	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928241	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928243	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928244	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928245	0.87[EUR][1000 genomes]
rs61928246	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928247	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928248	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61929725	0.81[EUR][1000 genomes]
rs61929728	0.81[EUR][1000 genomes]
rs61929731	0.91[EUR][1000 genomes]
rs6591821	0.89[EUR][1000 genomes]
rs6591822	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106670	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111395	1.00[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117206	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119961	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127454	1.00[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128040	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128970	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7482863	0.82[EUR][1000 genomes]
rs7928900	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932117	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939940	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943981	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944003	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944094	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945972	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949389	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949447	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17158453	MTA2	cis	cerebellum	SCAN
rs17158453	SNORD25	cis	parietal	SCAN
rs17158453	HRASLS3	cis	multi-tissue	Pritchard
rs17158453	PLA2G16	cis	cerebellum	SCAN
rs17158453	RASGRP2	cis	parietal	SCAN
rs17158453	FLRT1	cis	cerebellum	SCAN
rs17158453	SLC22A9	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63382000-63398400	Weak transcription	Small Intestine	intestine
2	chr11:63382200-63396400	Weak transcription	Spleen	Spleen
3	chr11:63382400-63396400	Weak transcription	Left Ventricle	heart
4	chr11:63382400-63398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:63382400-63409800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:63387800-63398400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:63388600-63396400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:63388800-63406400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:63388800-63414200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:63389000-63396400	Weak transcription	Primary B cells from cord blood	blood
11	chr11:63389000-63396600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:63389000-63398000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr11:63390000-63396400	Weak transcription	Brain Angular Gyrus	brain
14	chr11:63390000-63396400	Weak transcription	Brain Anterior Caudate	brain
15	chr11:63390200-63396400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:63390400-63398400	Weak transcription	Fetal Kidney	kidney
17	chr11:63390600-63396600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:63390600-63409600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:63390800-63414200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr11:63391000-63396600	Weak transcription	Gastric	stomach
21	chr11:63391200-63410400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:63391200-63418600	Weak transcription	Psoas Muscle	Psoas
23	chr11:63391400-63396400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr11:63391400-63396400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:63391400-63396400	Weak transcription	Pancreas	Pancrea
26	chr11:63391400-63396600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:63391400-63398400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr11:63391400-63398400	Weak transcription	Stomach Mucosa	stomach
29	chr11:63391600-63396400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:63391600-63396400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr11:63392800-63396400	Weak transcription	NHLF	lung
32	chr11:63393000-63396400	Weak transcription	Fetal Lung	lung
33	chr11:63393400-63396400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:63393600-63396400	Weak transcription	Brain Germinal Matrix	brain
35	chr11:63393600-63396400	Weak transcription	Fetal Brain Male	brain
36	chr11:63393600-63396400	Weak transcription	Fetal Brain Female	brain
37	chr11:63393600-63396400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr11:63393800-63396600	Weak transcription	Lung	lung
39	chr11:63393800-63426600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:63394000-63396400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:63394000-63396400	Weak transcription	Aorta	Aorta
42	chr11:63394000-63396400	Weak transcription	Brain Substantia Nigra	brain
43	chr11:63394000-63396400	Weak transcription	HSMMtube	muscle
44	chr11:63394000-63398400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr11:63394000-63406000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:63394000-63409200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:63394200-63396400	Weak transcription	Colonic Mucosa	Colon
48	chr11:63394200-63396600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr11:63394200-63400600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:63394200-63400800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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