Variant report

Variant	rs10877876
Chromosome Location	chr12:62952910-62952911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10128830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10128959	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10161549	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10219555	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10219765	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735907	0.90[EUR][1000 genomes]
rs10735909	0.89[EUR][1000 genomes]
rs10747963	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10747966	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10784299	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10784302	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10784303	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10784306	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784307	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];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877851	0.81[ASN][1000 genomes]
rs10877860	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877863	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877865	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877866	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877868	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877869	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877872	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10877873	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877878	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877880	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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877882	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877883	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877886	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877887	0.96[ASN][1000 genomes]
rs10877888	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11174493	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11174497	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11174507	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11174513	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11174520	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174534	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174538	0.91[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11174539	0.93[EUR][1000 genomes]
rs11174540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174542	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174545	0.85[ASN][1000 genomes]
rs11174550	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174559	0.82[ASN][1000 genomes]
rs11495588	0.82[ASN][1000 genomes]
rs12227568	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12300696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12305077	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12308140	0.84[MKK][hapmap]
rs12309683	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12357	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]
rs12371971	0.90[JPT][hapmap]
rs12371972	0.90[JPT][hapmap]
rs12578200	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12580048	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581171	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12809279	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12810119	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12829103	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1498713	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2029937	0.90[EUR][1000 genomes]
rs2047478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2047479	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2141777	0.80[ASN][1000 genomes]
rs2220980	0.91[EUR][1000 genomes]
rs35409044	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4763021	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4763174	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4763177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4763179	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763180	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6581452	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6581454	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7134302	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7136993	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71453871	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7294404	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7298782	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7302027	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7308021	0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7316612	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7957417	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7958597	0.81[CHB][hapmap]
rs7963657	0.96[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975183	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7975560	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv469418	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv559156	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10877876	NXPH4	cis	cerebellum	SCAN
rs10877876	TBK1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62866600-62953200	Weak transcription	Psoas Muscle	Psoas
2	chr12:62907000-62987200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:62915800-62971600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:62917200-62995000	Weak transcription	Fetal Heart	heart
5	chr12:62917400-62960000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:62919800-62970000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:62924400-62969800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr12:62924800-62967600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:62926200-62955800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:62927400-62967400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:62928000-62963400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:62928800-62995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:62932000-62957200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:62934800-62955400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:62935000-62955200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:62935400-62956400	Strong transcription	Placenta	Placenta
17	chr12:62935600-62955600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:62936000-62955200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:62936600-62956000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:62936800-62954600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:62938000-62995400	Weak transcription	Stomach Mucosa	stomach
22	chr12:62944600-62989000	Weak transcription	Colonic Mucosa	Colon
23	chr12:62945000-62966000	Weak transcription	Esophagus	oesophagus
24	chr12:62945800-62954800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:62946600-62955000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:62947400-62955000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:62947600-62953600	Strong transcription	Fetal Intestine Small	intestine
28	chr12:62947600-62953600	Strong transcription	Fetal Stomach	stomach
29	chr12:62948000-62956200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr12:62948200-62958600	Weak transcription	K562	blood
31	chr12:62949600-62955200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:62950200-62960800	Weak transcription	Brain Germinal Matrix	brain
33	chr12:62950200-62966800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:62950400-62995600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:62950600-62958400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:62950600-62975000	Weak transcription	Right Ventricle	heart
37	chr12:62950600-62982600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:62950600-62991200	Weak transcription	Gastric	stomach
39	chr12:62950600-62996200	Weak transcription	Small Intestine	intestine
40	chr12:62950800-62953000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:62950800-62968200	Weak transcription	Aorta	Aorta
42	chr12:62950800-62987600	Weak transcription	Pancreas	Pancrea
43	chr12:62950800-62995000	Weak transcription	NHEK	skin
44	chr12:62951000-62953200	Weak transcription	Fetal Brain Female	brain
45	chr12:62951000-62954000	Weak transcription	HUVEC	blood vessel
46	chr12:62951000-62954200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:62951000-62954200	Weak transcription	Brain Anterior Caudate	brain
48	chr12:62951000-62966000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:62951000-62987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:62951000-62995600	Weak transcription	Rectal Smooth Muscle	rectum

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