Variant report

Variant	rs11174557
Chromosome Location	chr12:62979216-62979217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62977946..62980694-chr12:63003640..63006233,2	MCF-7	breast:
2	chr12:62978537..62982109-chr12:62993246..62999032,10	MCF-7	breast:
3	chr12:62975073..62982220-chr12:62994233..63000379,9	K562	blood:
4	chr12:62977312..62980304-chr12:63191073..63192843,2	K562	blood:
5	chr12:62975484..62979404-chr12:62993353..62996237,5	K562	blood:
6	chr12:62978077..62985603-chr12:62994484..62999339,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199179	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000221949	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10444576	1.00[JPT][hapmap]
rs10877855	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877856	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877857	0.87[CEU][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877859	0.87[CEU][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877862	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877864	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877870	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174487	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs11174494	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174495	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174496	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11174498	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174504	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174514	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174517	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174518	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174527	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174537	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11174562	0.91[AFR][1000 genomes]
rs11174568	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11174569	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11174571	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11174575	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11174576	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11520127	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11613132	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11614022	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11614822	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12367878	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12369751	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12369961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12369985	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12370404	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12580567	1.00[CHB][hapmap]
rs17731893	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes]
rs17732089	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17732182	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2270732	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55833440	0.91[AFR][1000 genomes]
rs7296573	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7297093	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7301016	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7302094	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7302456	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303825	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7311952	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs73124315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73126004	0.91[AFR][1000 genomes]
rs73126024	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs73141014	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73141045	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7962519	0.91[CEU][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7975109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][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	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11174557	TBK1	cis	parietal	SCAN
rs11174557	MON2	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62907000-62987200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:62917200-62995000	Weak transcription	Fetal Heart	heart
3	chr12:62928800-62995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:62938000-62995400	Weak transcription	Stomach Mucosa	stomach
5	chr12:62944600-62989000	Weak transcription	Colonic Mucosa	Colon
6	chr12:62950400-62995600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:62950600-62982600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:62950600-62991200	Weak transcription	Gastric	stomach
9	chr12:62950600-62996200	Weak transcription	Small Intestine	intestine
10	chr12:62950800-62987600	Weak transcription	Pancreas	Pancrea
11	chr12:62950800-62995000	Weak transcription	NHEK	skin
12	chr12:62951000-62987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:62951000-62995600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:62951200-62979600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:62951200-62986800	Weak transcription	Brain Angular Gyrus	brain
16	chr12:62951200-62988600	Weak transcription	Spleen	Spleen
17	chr12:62951200-62995200	Weak transcription	Hela-S3	cervix
18	chr12:62951200-62995600	Weak transcription	HSMMtube	muscle
19	chr12:62951400-62995000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:62953400-62996000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:62954800-62989000	Weak transcription	Lung	lung
22	chr12:62954800-62995600	Weak transcription	Brain Anterior Caudate	brain
23	chr12:62955000-62987800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:62955200-62995200	Weak transcription	HepG2	liver
25	chr12:62955600-62995600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:62957000-62995600	Weak transcription	Fetal Brain Male	brain
27	chr12:62957200-62995600	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:62959400-62979800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:62959600-62995600	Weak transcription	NHLF	lung
30	chr12:62960000-62979600	Weak transcription	K562	blood
31	chr12:62960000-62982800	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:62961200-62995600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:62961400-62982600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:62961400-62989200	Weak transcription	Psoas Muscle	Psoas
35	chr12:62961400-62995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr12:62961400-62995600	Weak transcription	Brain Germinal Matrix	brain
37	chr12:62961600-62995600	Weak transcription	Fetal Brain Female	brain
38	chr12:62961800-62995600	Weak transcription	Brain Substantia Nigra	brain
39	chr12:62962000-62995600	Weak transcription	HMEC	breast
40	chr12:62962400-62982000	Weak transcription	HUVEC	blood vessel
41	chr12:62963200-62995600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:62964000-62995800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr12:62965400-62992800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:62965600-62982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:62965800-62982400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:62966000-62980600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:62966200-62982400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:62966200-62995600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:62966200-62995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:62966400-62985200	Weak transcription	Stomach Smooth Muscle	stomach

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