Variant report

Variant	rs12713775
Chromosome Location	chr2:73042768-73042769
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	chr2:73034831..73036995-chr2:73042272..73044592,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10211019	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1027848	0.95[EUR][1000 genomes]
rs10496186	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10865393	0.95[EUR][1000 genomes]
rs11126385	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1150500	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1161265	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs1161266	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1161267	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11684985	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs11894160	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12474728	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12622275	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12989141	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12996406	0.91[CEU][hapmap];0.80[AMR][1000 genomes]
rs13006497	1.00[CHD][hapmap]
rs13035731	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1396106	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1446895	0.91[CEU][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs1567230	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1995734	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2048170	0.93[EUR][1000 genomes]
rs2048171	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2135985	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2420880	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2420881	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2420883	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2421095	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4321391	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4852298	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4852883	1.00[CHD][hapmap]
rs4852886	1.00[CHD][hapmap]
rs4852893	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4852902	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546782	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6546783	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6546786	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6546788	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546789	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546790	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546791	0.94[EUR][1000 genomes]
rs6546792	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6730083	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6739002	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6750740	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6758431	0.95[EUR][1000 genomes]
rs6758542	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7571064	0.83[CEU][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap]
rs7580268	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7586787	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7588602	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7592155	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs925146	0.95[EUR][1000 genomes]
rs925147	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs925148	0.95[EUR][1000 genomes]
rs990569	0.91[CEU][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12713775	CYP26B1	cis	Whole Blood	GTEx
rs12713775	MPHOSPH10	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73034000-73049600	Weak transcription	Right Atrium	heart
2	chr2:73034400-73051600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:73036200-73050000	Weak transcription	Esophagus	oesophagus
4	chr2:73036200-73050600	Weak transcription	Left Ventricle	heart
5	chr2:73036400-73050800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:73036400-73051400	Weak transcription	Fetal Intestine Small	intestine
7	chr2:73036600-73051800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:73037000-73042800	Weak transcription	HepG2	liver
9	chr2:73037200-73051800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:73037400-73042800	Weak transcription	Hela-S3	cervix
11	chr2:73037400-73047200	Weak transcription	Fetal Lung	lung
12	chr2:73037600-73045800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:73038200-73044600	Weak transcription	Right Ventricle	heart
14	chr2:73038200-73051200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:73038400-73045600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:73038400-73048400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:73038400-73051200	Weak transcription	Fetal Stomach	stomach
18	chr2:73038400-73052000	Weak transcription	Aorta	Aorta
19	chr2:73040200-73048200	Weak transcription	Brain Germinal Matrix	brain
20	chr2:73040400-73044800	Weak transcription	Ovary	ovary
21	chr2:73041000-73049400	Weak transcription	Brain Angular Gyrus	brain
22	chr2:73041400-73049800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:73041400-73051400	Weak transcription	HSMM	muscle
24	chr2:73041600-73043800	Weak transcription	Fetal Heart	heart
25	chr2:73041600-73048400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:73041600-73049200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:73041600-73049400	Weak transcription	HMEC	breast
28	chr2:73041600-73049800	Weak transcription	Brain Anterior Caudate	brain
29	chr2:73041600-73050800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:73041600-73051200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:73041600-73051200	Weak transcription	NHDF-Ad	bronchial
32	chr2:73041600-73051400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:73041600-73051600	Weak transcription	HSMMtube	muscle
34	chr2:73041800-73042800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:73041800-73043000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:73041800-73043000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:73041800-73044600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:73041800-73046800	Weak transcription	NHEK	skin
39	chr2:73041800-73047400	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:73041800-73048400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:73041800-73048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:73041800-73049600	Weak transcription	Brain Substantia Nigra	brain
43	chr2:73041800-73051400	Weak transcription	Fetal Intestine Large	intestine
44	chr2:73042400-73042800	Enhancers	A549	lung
45	chr2:73042600-73050000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:73042600-73051200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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