Variant report

Variant	rs12357
Chromosome Location	chr12:62986620-62986621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62979450..62981862-chr12:62984868..62986770,2	K562	blood:
2	chr12:62983638..62988242-chr12:62993831..62996165,4	K562	blood:
3	chr12:62982029..62985002-chr12:62986611..62990117,5	K562	blood:
4	chr12:62977954..62981862-chr12:62984868..62986789,3	K562	blood:
5	chr12:62981599..62984459-chr12:62985303..62987502,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000061987	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10128830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10128959	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10161549	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10219555	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10219765	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10735907	0.85[EUR][1000 genomes]
rs10735909	0.84[EUR][1000 genomes]
rs10747963	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs10747966	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10784299	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10784302	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10784303	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10784306	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10784307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877860	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877863	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877865	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877866	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877868	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10877869	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877872	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10877873	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877876	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877878	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877882	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877883	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877886	0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877887	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877888	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174493	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11174497	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11174507	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11174513	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11174520	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11174534	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11174538	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11174539	0.87[EUR][1000 genomes]
rs11174540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174542	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174545	0.84[ASN][1000 genomes]
rs11174550	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11174559	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11495588	0.81[ASN][1000 genomes]
rs12227568	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12300696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12305077	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12309683	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12371971	0.90[JPT][hapmap]
rs12371972	0.90[JPT][hapmap]
rs12578200	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12580048	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581171	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12809279	0.80[ASN][1000 genomes]
rs12810119	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12829103	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498713	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2029937	0.85[EUR][1000 genomes]
rs2047478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2047479	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2220980	0.86[EUR][1000 genomes]
rs35409044	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4763021	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4763174	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763179	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4763180	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581452	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581454	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7134302	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7136993	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71453871	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294404	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7298782	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7302027	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7308021	0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs7316612	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7957417	0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7958597	0.81[CHB][hapmap]
rs7963657	0.96[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975183	0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7975560	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][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
rs12357	NXPH4	cis	cerebellum	SCAN
rs12357	TBK1	cis	cerebellum	SCAN

Chromatin state (count:108 , 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	chr12:62950600-62991200	Weak transcription	Gastric	stomach
8	chr12:62950600-62996200	Weak transcription	Small Intestine	intestine
9	chr12:62950800-62987600	Weak transcription	Pancreas	Pancrea
10	chr12:62950800-62995000	Weak transcription	NHEK	skin
11	chr12:62951000-62987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:62951000-62995600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:62951200-62986800	Weak transcription	Brain Angular Gyrus	brain
14	chr12:62951200-62988600	Weak transcription	Spleen	Spleen
15	chr12:62951200-62995200	Weak transcription	Hela-S3	cervix
16	chr12:62951200-62995600	Weak transcription	HSMMtube	muscle
17	chr12:62951400-62995000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:62953400-62996000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:62954800-62989000	Weak transcription	Lung	lung
20	chr12:62954800-62995600	Weak transcription	Brain Anterior Caudate	brain
21	chr12:62955000-62987800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:62955200-62995200	Weak transcription	HepG2	liver
23	chr12:62955600-62995600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:62957000-62995600	Weak transcription	Fetal Brain Male	brain
25	chr12:62957200-62995600	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:62959600-62995600	Weak transcription	NHLF	lung
27	chr12:62961200-62995600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:62961400-62989200	Weak transcription	Psoas Muscle	Psoas
29	chr12:62961400-62995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:62961400-62995600	Weak transcription	Brain Germinal Matrix	brain
31	chr12:62961600-62995600	Weak transcription	Fetal Brain Female	brain
32	chr12:62961800-62995600	Weak transcription	Brain Substantia Nigra	brain
33	chr12:62962000-62995600	Weak transcription	HMEC	breast
34	chr12:62963200-62995600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:62964000-62995800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:62965400-62992800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:62966200-62995600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:62966200-62995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:62966400-62995600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:62966400-62995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:62966600-62991000	Weak transcription	Adipose Nuclei	Adipose
42	chr12:62966600-62995600	Weak transcription	Thymus	Thymus
43	chr12:62966600-62996000	Weak transcription	Esophagus	oesophagus
44	chr12:62969000-62995600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:62969000-62996000	Weak transcription	Left Ventricle	heart
46	chr12:62969000-62996000	Weak transcription	Ovary	ovary
47	chr12:62970000-62995200	Weak transcription	Fetal Lung	lung
48	chr12:62972200-62988800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr12:62976400-62987400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr12:62977200-62993400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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