Variant report

Variant	rs10865392
Chromosome Location	chr2:72801753-72801754
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:72797499..72799587-chr2:72800647..72803483,4	MCF-7	breast:

Extended variants
information (count: 172 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:165)

rs_ID	r²[population]
rs10183056	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs10186080	1.00[ASN][1000 genomes]
rs10190674	1.00[ASN][1000 genomes]
rs10203965	1.00[ASN][1000 genomes]
rs10206555	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs10211019	1.00[ASN][1000 genomes]
rs10460572	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496186	0.92[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865391	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126370	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126371	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126372	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126373	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126374	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126385	1.00[ASN][1000 genomes]
rs11684985	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686713	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs11894160	1.00[ASN][1000 genomes]
rs12052508	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12471136	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471312	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs12476130	0.92[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476397	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs12618390	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713772	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713773	0.91[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713774	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989141	1.00[ASN][1000 genomes]
rs12996406	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs12998681	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006497	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs13008041	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008258	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13016873	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383535	1.00[ASN][1000 genomes]
rs13424607	1.00[ASN][1000 genomes]
rs1400580	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400582	0.92[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs1446888	0.92[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446889	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446890	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446891	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446892	0.92[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446893	0.92[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446895	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517181	0.92[CEU][hapmap]
rs1568145	1.00[ASN][1000 genomes]
rs1711838	0.92[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992799	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995734	1.00[ASN][1000 genomes]
rs2048171	0.92[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138683	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2203679	0.82[GIH][hapmap]
rs2420565	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3106879	1.00[ASN][1000 genomes]
rs3106880	1.00[ASN][1000 genomes]
rs3115351	0.84[GIH][hapmap]
rs34127669	1.00[ASN][1000 genomes]
rs4144318	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407272	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852291	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852292	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4852293	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852294	1.00[ASN][1000 genomes]
rs4852298	0.92[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852872	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852873	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs4852875	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852876	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852877	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852878	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852879	1.00[CHD][hapmap];0.84[GIH][hapmap]
rs4852880	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852883	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs4852886	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs4852893	1.00[ASN][1000 genomes]
rs581976	1.00[ASN][1000 genomes]
rs583673	0.91[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585653	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs585938	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587431	1.00[ASN][1000 genomes]
rs59095814	1.00[ASN][1000 genomes]
rs597799	1.00[ASN][1000 genomes]
rs598547	1.00[ASN][1000 genomes]
rs602465	1.00[ASN][1000 genomes]
rs603324	1.00[ASN][1000 genomes]
rs613880	1.00[ASN][1000 genomes]
rs614653	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs619343	1.00[ASN][1000 genomes]
rs62149282	1.00[ASN][1000 genomes]
rs623095	1.00[ASN][1000 genomes]
rs625434	1.00[ASN][1000 genomes]
rs631550	1.00[ASN][1000 genomes]
rs632670	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs634476	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs634574	0.91[CEU][hapmap];1.00[ASN][1000 genomes]
rs634785	1.00[ASN][1000 genomes]
rs634929	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs636319	1.00[ASN][1000 genomes]
rs636332	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs636734	0.92[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs641123	0.92[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs642652	0.84[GIH][hapmap]
rs642847	1.00[ASN][1000 genomes]
rs645489	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs646357	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs647269	0.91[CEU][hapmap];1.00[ASN][1000 genomes]
rs650352	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs653220	0.89[GIH][hapmap]
rs653842	1.00[ASN][1000 genomes]
rs654157	1.00[ASN][1000 genomes]
rs6546765	1.00[ASN][1000 genomes]
rs6546776	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546777	0.92[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546778	0.92[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546779	0.92[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546782	0.92[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546783	0.92[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656370	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs656440	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs658067	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs661395	1.00[ASN][1000 genomes]
rs663218	0.84[GIH][hapmap]
rs664652	1.00[ASN][1000 genomes]
rs666361	0.90[CEU][hapmap];1.00[ASN][1000 genomes]
rs669074	1.00[ASN][1000 genomes]
rs6707435	1.00[ASN][1000 genomes]
rs6714580	1.00[ASN][1000 genomes]
rs671550	1.00[ASN][1000 genomes]
rs671721	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs6736305	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs6739002	1.00[ASN][1000 genomes]
rs6741956	1.00[ASN][1000 genomes]
rs6742088	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742312	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747378	0.92[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674863	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs6750766	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758593	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs6761075	0.90[EUR][1000 genomes]
rs678684	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs680380	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs681574	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs681908	1.00[ASN][1000 genomes]
rs683328	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs684673	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs687325	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs687371	1.00[ASN][1000 genomes]
rs688433	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs7420391	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560529	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560599	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565198	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571064	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580268	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs7588602	1.00[ASN][1000 genomes]
rs7591025	0.92[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591303	0.92[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592155	1.00[ASN][1000 genomes]
rs7598238	0.92[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601020	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601318	0.92[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603797	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983928	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990569	0.92[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1008335	chr2:72561463-72819704	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv874264	chr2:72593243-72901170	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv582208	chr2:72690622-72835886	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv834257	chr2:72701083-72853548	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10865392	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72775000-72808800	Weak transcription	Ovary	ovary
2	chr2:72786000-72803800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr2:72789200-72803600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:72789400-72803400	Weak transcription	Adipose Nuclei	Adipose
5	chr2:72789800-72803600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:72790000-72803200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:72790000-72804200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:72795200-72803200	Weak transcription	Osteobl	bone
9	chr2:72796400-72803800	Weak transcription	HUVEC	blood vessel
10	chr2:72797200-72806800	Enhancers	A549	lung
11	chr2:72798200-72803400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:72798400-72803200	Weak transcription	HSMM	muscle
13	chr2:72799600-72802200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:72799600-72803400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:72799600-72807400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:72800000-72803400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:72800000-72803600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:72800400-72803400	Weak transcription	HSMMtube	muscle
19	chr2:72800600-72802200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:72800600-72803400	Weak transcription	NH-A	brain
21	chr2:72800800-72803800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:72800800-72806000	Weak transcription	Fetal Heart	heart
23	chr2:72801000-72802800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr2:72801000-72803000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:72801000-72803800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr2:72801200-72803400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:72801400-72802600	Enhancers	HepG2	liver
28	chr2:72801400-72803600	Weak transcription	Placenta	Placenta
29	chr2:72801600-72801800	Enhancers	Fetal Lung	lung

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