Variant report

Variant	rs3861890
Chromosome Location	chr12:67671926-67671927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:67671859..67674650-chr12:67694307..67697083,2	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10506544	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1060350	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1066389	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1066390	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1066391	0.95[ASN][1000 genomes]
rs1066396	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1066398	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1066399	0.95[ASN][1000 genomes]
rs1066404	0.97[ASN][1000 genomes]
rs10784619	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784624	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1082700	0.95[ASN][1000 genomes]
rs1082710	0.90[ASN][1000 genomes]
rs10878596	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878601	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1092600	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1112445	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11176647	0.93[ASN][1000 genomes]
rs11176657	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176677	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176683	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176690	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11176695	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11176700	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1136080	0.95[ASN][1000 genomes]
rs1137465	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1143954	0.95[ASN][1000 genomes]
rs1143956	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1144939	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1152877	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152895	0.95[ASN][1000 genomes]
rs1152896	0.97[ASN][1000 genomes]
rs1152897	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152898	0.98[ASN][1000 genomes]
rs1152901	0.98[ASN][1000 genomes]
rs1152902	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1161085	0.95[ASN][1000 genomes]
rs1161087	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1161089	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1161090	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1183126	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1184743	0.92[ASN][1000 genomes]
rs1185918	0.89[ASN][1000 genomes]
rs12366819	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12369715	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12370954	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12422358	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12422968	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12424158	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252364	0.95[ASN][1000 genomes]
rs1252386	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1252387	0.89[ASN][1000 genomes]
rs1252388	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1252402	0.95[ASN][1000 genomes]
rs1252405	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252407	0.97[ASN][1000 genomes]
rs1252419	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252422	0.97[ASN][1000 genomes]
rs1252424	0.93[ASN][1000 genomes]
rs12580790	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1272089	0.89[ASN][1000 genomes]
rs1392587	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1500431	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1561333	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1583648	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1612693	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1697232	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1697233	0.97[ASN][1000 genomes]
rs17781745	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1921000	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1985476	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2028213	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2091698	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2118311	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2118533	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2178466	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2248751	0.97[ASN][1000 genomes]
rs2438109	0.95[ASN][1000 genomes]
rs2576941	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4913538	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4913540	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4913541	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61918267	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61920672	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs698123	0.97[ASN][1000 genomes]
rs710626	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs710627	0.97[ASN][1000 genomes]
rs710628	0.97[ASN][1000 genomes]
rs710629	0.90[ASN][1000 genomes]
rs710630	0.95[ASN][1000 genomes]
rs710800	0.85[ASN][1000 genomes]
rs7134743	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs775306	0.98[ASN][1000 genomes]
rs775309	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775312	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775644	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs775645	0.89[ASN][1000 genomes]
rs775651	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs775652	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs775655	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs775660	0.97[ASN][1000 genomes]
rs796522	0.85[ASN][1000 genomes]
rs7968645	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7973565	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7977430	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs811820	0.97[ASN][1000 genomes]
rs811827	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs814290	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3861890	CAND1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67664600-67684000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:67664800-67694400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:67664800-67699600	Weak transcription	Aorta	Aorta
4	chr12:67665200-67673000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr12:67665200-67675400	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr12:67665200-67675800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr12:67665200-67675800	Weak transcription	Placenta	Placenta
8	chr12:67665200-67675800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:67665200-67676200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:67665200-67678400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:67665200-67684400	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:67665200-67684600	Weak transcription	Thymus	Thymus
13	chr12:67665200-67690200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:67665200-67699000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:67665400-67687600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr12:67665600-67672000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:67665600-67672000	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr12:67665600-67673800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:67665600-67674600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:67666000-67688400	Weak transcription	Fetal Kidney	kidney
21	chr12:67666000-67701000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:67666800-67676200	Weak transcription	Fetal Intestine Large	intestine
23	chr12:67667200-67672200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:67667600-67682600	Weak transcription	Lung	lung
25	chr12:67667800-67673200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr12:67668400-67674400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:67668400-67675800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:67668400-67678400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr12:67668400-67688200	Weak transcription	HUVEC	blood vessel
30	chr12:67668600-67675800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:67668800-67678200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:67669000-67672400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr12:67669000-67675400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:67669000-67675400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr12:67669200-67673200	Enhancers	Ovary	ovary
36	chr12:67669200-67673400	Weak transcription	Liver	Liver
37	chr12:67669400-67672000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr12:67669400-67672000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr12:67669400-67675800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:67669400-67683000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:67669600-67672000	Weak transcription	Gastric	stomach
42	chr12:67669600-67673600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr12:67669600-67674000	Weak transcription	Brain Hippocampus Middle	brain
44	chr12:67669600-67675600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:67669800-67672000	Genic enhancers	Primary T cells from cord blood	blood
46	chr12:67669800-67672800	Weak transcription	Small Intestine	intestine
47	chr12:67669800-67673600	Weak transcription	Adipose Nuclei	Adipose
48	chr12:67669800-67675600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:67669800-67678000	Weak transcription	NH-A	brain
50	chr12:67670000-67672600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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