Variant report

Variant	rs12670415
Chromosome Location	chr7:27602223-27602224
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	chr7:27596213..27599190-chr7:27601931..27603568,2	MCF-7	breast:

Extended variants
information (count: 180 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:179)

rs_ID	r²[population]
rs1005128	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1009252	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1014373	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1015265	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1015750	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1030003	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10447552	1.00[CEU][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10486548	0.81[CEU][hapmap]
rs1052724	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1052741	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10807841	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10951169	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10951171	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10951172	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10951175	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1111647	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1115346	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1115347	0.85[EUR][1000 genomes]
rs11526176	0.93[ASN][1000 genomes]
rs11762342	0.86[EUR][1000 genomes]
rs11763449	0.86[EUR][1000 genomes]
rs11764753	0.81[CEU][hapmap]
rs11767188	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11973492	0.84[EUR][1000 genomes]
rs12155430	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12530626	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12535844	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12537499	1.00[CEU][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12539707	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12540276	0.93[ASN][1000 genomes]
rs12665991	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12667235	1.00[CEU][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12667610	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12668430	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12670771	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12672811	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12673949	0.81[CEU][hapmap];0.91[AMR][1000 genomes]
rs12700813	0.93[ASN][1000 genomes]
rs12700815	0.93[ASN][1000 genomes]
rs12700817	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12700819	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12700822	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12700825	0.81[CEU][hapmap]
rs12700826	1.00[CEU][hapmap]
rs12700829	0.82[CEU][hapmap]
rs12700830	0.81[CEU][hapmap]
rs13226102	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13227873	0.93[ASN][1000 genomes]
rs13242248	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13244903	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13246464	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs13308974	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1357760	0.93[ASN][1000 genomes]
rs1404276	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1404278	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1404282	0.81[CEU][hapmap];0.91[AMR][1000 genomes]
rs1524526	0.84[ASN][1000 genomes]
rs1524529	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1524530	0.93[ASN][1000 genomes]
rs1524531	0.93[ASN][1000 genomes]
rs1524532	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1524533	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1554641	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1608663	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1608664	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1851911	0.97[ASN][1000 genomes]
rs1851912	0.84[ASN][1000 genomes]
rs1851913	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880370	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1980329	1.00[CEU][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1980330	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1986243	0.93[ASN][1000 genomes]
rs2037638	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2041714	1.00[CEU][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2041715	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2080245	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2080246	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2091171	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2098315	0.95[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2098316	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2110526	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2110528	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2391443	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391444	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2391445	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2391446	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2391447	0.82[CEU][hapmap]
rs2391449	0.81[EUR][1000 genomes]
rs2391451	0.82[CEU][hapmap]
rs2391452	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2391453	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2391454	0.81[CEU][hapmap]
rs28416309	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28429439	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34886410	0.93[ASN][1000 genomes]
rs3847001	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3925338	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4140899	1.00[CEU][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs42085	1.00[CEU][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs42087	0.81[CEU][hapmap]
rs4348389	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4719898	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4719899	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4719900	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4719902	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4722719	1.00[CEU][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4722724	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4722726	0.80[CEU][hapmap]
rs4722728	1.00[CEU][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56024263	0.84[EUR][1000 genomes]
rs56139857	0.84[EUR][1000 genomes]
rs6415251	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs6462026	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6462029	0.95[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6462031	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6462032	0.93[ASN][1000 genomes]
rs6462033	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6462034	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6462036	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6462037	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6462038	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6462039	0.81[CEU][hapmap]
rs6943883	0.81[CEU][hapmap]
rs6945993	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6946075	0.93[ASN][1000 genomes]
rs6947731	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6948460	0.84[AMR][1000 genomes]
rs6948814	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6949496	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6954905	0.82[CEU][hapmap]
rs6955074	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6956484	0.93[ASN][1000 genomes]
rs6957378	0.81[CEU][hapmap]
rs6957674	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6958467	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6958747	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs6959126	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6959495	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6960834	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6963421	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6963585	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6964190	0.93[ASN][1000 genomes]
rs6966587	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6966918	0.93[ASN][1000 genomes]
rs6970104	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6974052	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6974387	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6974932	1.00[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6976178	0.81[EUR][1000 genomes]
rs6980382	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs723699	0.93[ASN][1000 genomes]
rs723700	0.93[ASN][1000 genomes]
rs7455882	0.93[ASN][1000 genomes]
rs759269	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs759270	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs759271	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7779240	0.93[ASN][1000 genomes]
rs7780431	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7783447	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7786973	0.81[CEU][hapmap];0.91[AMR][1000 genomes]
rs7789788	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7790498	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7794292	0.84[ASN][1000 genomes]
rs7806415	0.80[CEU][hapmap]
rs7806605	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7806812	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7809748	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7811436	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs940525	0.93[ASN][1000 genomes]
rs940526	0.93[ASN][1000 genomes]
rs961723	0.81[CEU][hapmap]
rs961725	0.82[CEU][hapmap]
rs9639552	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9639553	0.95[CEU][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9639559	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9639560	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs974883	0.82[CEU][hapmap];0.91[AMR][1000 genomes]
rs978447	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs986706	1.00[CEU][hapmap]

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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12670415	HIBADH	cis	multi-tissue	Pritchard
rs12670415	HIBADH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27559400-27627800	Weak transcription	Psoas Muscle	Psoas
2	chr7:27580600-27615000	Weak transcription	Aorta	Aorta
3	chr7:27581400-27617400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:27581600-27602800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr7:27581800-27603000	Weak transcription	Fetal Lung	lung
6	chr7:27582200-27603000	Weak transcription	Primary T cells from cord blood	blood
7	chr7:27582400-27650800	Weak transcription	Left Ventricle	heart
8	chr7:27582800-27604800	Weak transcription	Fetal Kidney	kidney
9	chr7:27582800-27615000	Weak transcription	Placenta	Placenta
10	chr7:27582800-27615200	Weak transcription	Ovary	ovary
11	chr7:27587400-27602600	Weak transcription	Adipose Nuclei	Adipose
12	chr7:27587800-27602600	Weak transcription	HSMM	muscle
13	chr7:27595800-27603000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:27596000-27602600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:27600600-27645600	Weak transcription	Colon Smooth Muscle	Colon
16	chr7:27601000-27603200	Weak transcription	Liver	Liver
17	chr7:27601200-27602600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr7:27601200-27609600	Weak transcription	Osteobl	bone
19	chr7:27601600-27602800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:27602200-27602400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:27602200-27602400	ZNF genes & repeats	Fetal Intestine Small	intestine
22	chr7:27602200-27602400	Enhancers	Thymus	Thymus
23	chr7:27602200-27602800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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