Variant report

Variant	rs1252410
Chromosome Location	chr12:67666501-67666502
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	chr12:67639415..67642144-chr12:67665487..67667188,2	MCF-7	breast:
2	chr12:67665523..67668331-chr12:67690936..67692642,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10506545	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1066387	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066388	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066394	0.94[AFR][1000 genomes]
rs1066395	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10784625	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1082701	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1082702	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1082708	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1082709	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1082711	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1092475	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11176678	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1143758	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1143947	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1143948	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1152900	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1161088	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1161092	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1177317	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252414	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252418	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1252423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1272090	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1500433	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1561334	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1621634	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1658780	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1985475	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2438108	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs710622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs710623	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs710624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs710797	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs710798	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs710801	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs775307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs775308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs775310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs775628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775634	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs775635	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs775646	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs775647	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs775648	0.87[AFR][1000 genomes]
rs775650	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs775653	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs775654	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs775656	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs775657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs775658	1.00[ASN][1000 genomes]
rs775659	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs775661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957112	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7962358	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7962587	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs796508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7976111	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs800166	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs800167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs812325	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs812326	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs983630	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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
rs1252410	CAND1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67664400-67666600	Weak transcription	Lung	lung
2	chr12:67664400-67666600	Weak transcription	Small Intestine	intestine
3	chr12:67664400-67666600	Weak transcription	Spleen	Spleen
4	chr12:67664400-67666800	Enhancers	Brain Substantia Nigra	brain
5	chr12:67664400-67669000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:67664400-67669200	Weak transcription	Gastric	stomach
7	chr12:67664400-67669400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:67664600-67666600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr12:67664600-67684000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:67664800-67666600	Enhancers	Brain Hippocampus Middle	brain
11	chr12:67664800-67666800	Enhancers	Primary B cells from cord blood	blood
12	chr12:67664800-67694400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:67664800-67699600	Weak transcription	Aorta	Aorta
14	chr12:67665200-67666600	Weak transcription	Psoas Muscle	Psoas
15	chr12:67665200-67666800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:67665200-67666800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:67665200-67666800	Enhancers	Adipose Nuclei	Adipose
18	chr12:67665200-67666800	Enhancers	Fetal Heart	heart
19	chr12:67665200-67667000	Weak transcription	Fetal Thymus	thymus
20	chr12:67665200-67667200	Enhancers	Rectal Smooth Muscle	rectum
21	chr12:67665200-67667400	Weak transcription	Stomach Mucosa	stomach
22	chr12:67665200-67667800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:67665200-67668000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:67665200-67668600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:67665200-67669000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:67665200-67669400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:67665200-67670600	Weak transcription	Brain Angular Gyrus	brain
28	chr12:67665200-67671200	Weak transcription	Right Atrium	heart
29	chr12:67665200-67671800	Weak transcription	Esophagus	oesophagus
30	chr12:67665200-67673000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:67665200-67675400	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr12:67665200-67675800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr12:67665200-67675800	Weak transcription	Placenta	Placenta
34	chr12:67665200-67675800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr12:67665200-67676200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:67665200-67678400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:67665200-67684400	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:67665200-67684600	Weak transcription	Thymus	Thymus
39	chr12:67665200-67690200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr12:67665200-67699000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:67665400-67667200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr12:67665400-67668200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr12:67665400-67669600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:67665400-67670200	Weak transcription	HSMMtube	muscle
45	chr12:67665400-67671200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:67665400-67687600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:67665600-67666600	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr12:67665600-67666600	Enhancers	Fetal Brain Male	brain
49	chr12:67665600-67666600	Genic enhancers	Hela-S3	cervix
50	chr12:67665600-67667200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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