Variant report

Variant	rs1143956
Chromosome Location	chr12:67690435-67690436
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10506544	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1060350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1066389	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1066390	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1066391	0.98[ASN][1000 genomes]
rs1066396	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1066398	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1066399	0.98[ASN][1000 genomes]
rs1066404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10784619	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784624	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1082700	0.98[ASN][1000 genomes]
rs1082710	0.93[ASN][1000 genomes]
rs10878596	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878601	0.81[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1092600	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1112445	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176647	0.93[ASN][1000 genomes]
rs11176657	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176677	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176690	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176695	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176700	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1125748	0.81[ASN][1000 genomes]
rs1136080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1137465	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1143954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1144939	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152877	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1152896	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1152897	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1152901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1152902	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1161085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1161087	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1161089	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1161090	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1183126	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1184743	0.95[ASN][1000 genomes]
rs1185918	0.92[ASN][1000 genomes]
rs12366819	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12369715	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12370954	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12422358	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12422968	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12424158	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252364	0.98[ASN][1000 genomes]
rs1252386	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1252387	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1252388	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1252402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1252405	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1252419	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252422	0.99[ASN][1000 genomes]
rs1252424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12580790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1272089	0.92[ASN][1000 genomes]
rs1392587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500431	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1561333	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1583648	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1612693	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1697232	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1697233	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17781745	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1921000	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1985476	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2028213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2091698	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2118311	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2118533	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2178466	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2248751	1.00[ASN][1000 genomes]
rs2438109	0.95[ASN][1000 genomes]
rs2576941	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3861890	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4913538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4913540	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4913541	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61918267	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61920672	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs698123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs710626	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs710627	0.97[ASN][1000 genomes]
rs710628	0.97[ASN][1000 genomes]
rs710629	0.93[ASN][1000 genomes]
rs710630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs710800	0.89[ASN][1000 genomes]
rs7134743	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs775306	0.98[ASN][1000 genomes]
rs775309	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775644	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs775645	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs775651	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs775652	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs775655	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs775660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs796522	0.89[ASN][1000 genomes]
rs7968645	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7973565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7977430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs811820	1.00[ASN][1000 genomes]
rs811827	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs814290	1.00[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	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv525023	chr12:67672870-67708669	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1143956	CAND1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67664800-67694400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:67664800-67699600	Weak transcription	Aorta	Aorta
3	chr12:67665200-67699000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:67666000-67701000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:67670000-67699200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:67670200-67698200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:67671400-67698400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:67671600-67691800	Weak transcription	Fetal Brain Male	brain
9	chr12:67672200-67699000	Weak transcription	Esophagus	oesophagus
10	chr12:67672400-67693800	Weak transcription	Psoas Muscle	Psoas
11	chr12:67673200-67699400	Weak transcription	Small Intestine	intestine
12	chr12:67674200-67694000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:67674400-67696000	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:67674600-67708000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:67674800-67697800	Strong transcription	Fetal Thymus	thymus
16	chr12:67674800-67706400	Weak transcription	Stomach Mucosa	stomach
17	chr12:67675600-67694600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:67676200-67691000	Weak transcription	HMEC	breast
19	chr12:67676800-67691800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:67678600-67699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:67679000-67692200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:67679600-67692200	Weak transcription	Fetal Brain Female	brain
23	chr12:67680000-67696000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:67681000-67698200	Weak transcription	Brain Substantia Nigra	brain
25	chr12:67681000-67714200	Weak transcription	Spleen	Spleen
26	chr12:67681200-67699200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:67682200-67699400	Weak transcription	Pancreas	Pancrea
28	chr12:67682200-67709000	Strong transcription	Dnd41	blood
29	chr12:67682200-67715200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:67682400-67707600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr12:67682600-67710600	Weak transcription	Right Ventricle	heart
32	chr12:67683400-67710600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:67684400-67708400	Strong transcription	GM12878-XiMat	blood
34	chr12:67684600-67692000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr12:67684800-67691600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr12:67684800-67693800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:67684800-67698400	Weak transcription	Lung	lung
38	chr12:67684800-67698800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:67684800-67699000	Weak transcription	Gastric	stomach
40	chr12:67685000-67691200	Weak transcription	Brain Anterior Caudate	brain
41	chr12:67685000-67691200	Weak transcription	HSMMtube	muscle
42	chr12:67685000-67691800	Weak transcription	Fetal Lung	lung
43	chr12:67685000-67698800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:67685200-67690800	Weak transcription	Hela-S3	cervix
45	chr12:67685200-67691600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:67685200-67692600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:67685200-67696200	Weak transcription	Brain Germinal Matrix	brain
48	chr12:67685800-67708000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:67686000-67717000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:67686200-67694600	Strong transcription	Primary hematopoietic stem cells	blood

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