Variant report

Variant	rs1252407
Chromosome Location	chr12:67667998-67667999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:67665523..67668331-chr12:67690936..67692642,2	K562	blood:

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10506544	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1060350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1066389	0.95[ASN][1000 genomes]
rs1066390	0.95[ASN][1000 genomes]
rs1066391	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1066396	0.95[ASN][1000 genomes]
rs1066398	0.95[ASN][1000 genomes]
rs1066399	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1066404	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784619	0.98[ASN][1000 genomes]
rs10784624	0.80[ASN][1000 genomes]
rs1082700	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1082710	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10878596	0.97[ASN][1000 genomes]
rs10878601	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1092600	0.95[ASN][1000 genomes]
rs1112445	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11176647	0.93[ASN][1000 genomes]
rs11176657	0.93[ASN][1000 genomes]
rs11176677	0.95[ASN][1000 genomes]
rs11176683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11176690	0.90[ASN][1000 genomes]
rs11176695	0.89[ASN][1000 genomes]
rs11176700	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1136080	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1137465	0.95[ASN][1000 genomes]
rs1143954	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1143956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1144939	0.92[ASN][1000 genomes]
rs1152877	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1152895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152896	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1152897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1152898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1161085	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1161087	0.85[ASN][1000 genomes]
rs1161089	0.95[ASN][1000 genomes]
rs1161090	0.95[ASN][1000 genomes]
rs1161092	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1183126	0.92[ASN][1000 genomes]
rs1184743	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1185918	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12366819	0.95[ASN][1000 genomes]
rs12369715	0.89[ASN][1000 genomes]
rs12370954	0.94[ASN][1000 genomes]
rs12422358	0.89[ASN][1000 genomes]
rs12422968	0.95[ASN][1000 genomes]
rs12424158	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1252364	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1252386	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1252387	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1252388	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1252402	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1252405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1252419	0.97[ASN][1000 genomes]
rs1252422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1252424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12580790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1272089	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1392587	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1500431	0.90[ASN][1000 genomes]
rs1583648	0.90[ASN][1000 genomes]
rs1612693	0.89[ASN][1000 genomes]
rs1697232	0.95[ASN][1000 genomes]
rs1697233	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17781745	0.92[ASN][1000 genomes]
rs1921000	0.85[ASN][1000 genomes]
rs1985476	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2028213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2091698	0.94[ASN][1000 genomes]
rs2118311	0.90[ASN][1000 genomes]
rs2178466	0.81[ASN][1000 genomes]
rs2248751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2438109	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2576941	0.97[ASN][1000 genomes]
rs3736630	0.83[YRI][hapmap]
rs3861890	0.97[ASN][1000 genomes]
rs4913538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4913540	0.95[ASN][1000 genomes]
rs4913541	0.90[ASN][1000 genomes]
rs61918267	0.96[ASN][1000 genomes]
rs61920672	0.98[ASN][1000 genomes]
rs698123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs710626	0.98[ASN][1000 genomes]
rs710627	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs710628	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs710629	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs710630	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs710800	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7134743	0.89[ASN][1000 genomes]
rs775306	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs775309	0.97[ASN][1000 genomes]
rs775312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs775644	0.90[ASN][1000 genomes]
rs775645	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs775651	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs775652	0.85[ASN][1000 genomes]
rs775655	0.85[ASN][1000 genomes]
rs775660	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs796522	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7968645	0.98[ASN][1000 genomes]
rs7973565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7977430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs811820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs811827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs814290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1252407	CAND1	Cis_1M	lymphoblastoid	RTeQTL
rs1252407	NA	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67664400-67669000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:67664400-67669200	Weak transcription	Gastric	stomach
3	chr12:67664400-67669400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:67664600-67684000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:67664800-67694400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:67664800-67699600	Weak transcription	Aorta	Aorta
7	chr12:67665200-67668000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:67665200-67668600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:67665200-67669000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:67665200-67669400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:67665200-67670600	Weak transcription	Brain Angular Gyrus	brain
12	chr12:67665200-67671200	Weak transcription	Right Atrium	heart
13	chr12:67665200-67671800	Weak transcription	Esophagus	oesophagus
14	chr12:67665200-67673000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:67665200-67675400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr12:67665200-67675800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr12:67665200-67675800	Weak transcription	Placenta	Placenta
18	chr12:67665200-67675800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:67665200-67676200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:67665200-67678400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:67665200-67684400	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:67665200-67684600	Weak transcription	Thymus	Thymus
23	chr12:67665200-67690200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:67665200-67699000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:67665400-67668200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr12:67665400-67669600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:67665400-67670200	Weak transcription	HSMMtube	muscle
28	chr12:67665400-67671200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:67665400-67687600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:67665600-67668000	Enhancers	Duodenum Mucosa	Duodenum
31	chr12:67665600-67668200	Enhancers	Primary T cells from cord blood	blood
32	chr12:67665600-67668200	Enhancers	NHEK	skin
33	chr12:67665600-67669800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:67665600-67672000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:67665600-67672000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr12:67665600-67673800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:67665600-67674600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:67665800-67668400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:67666000-67668000	Weak transcription	Brain Anterior Caudate	brain
40	chr12:67666000-67668000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr12:67666000-67668600	Weak transcription	NHDF-Ad	bronchial
42	chr12:67666000-67670000	Weak transcription	Fetal Stomach	stomach
43	chr12:67666000-67670200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:67666000-67671000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:67666000-67671200	Weak transcription	Fetal Brain Female	brain
46	chr12:67666000-67688400	Weak transcription	Fetal Kidney	kidney
47	chr12:67666000-67701000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:67666200-67668000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr12:67666200-67668200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr12:67666200-67668200	Weak transcription	Rectal Mucosa Donor 29	rectum

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