Variant report

Variant	rs12539707
Chromosome Location	chr7:27626165-27626166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1005128	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1009252	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1014373	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1015750	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1030003	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1052724	0.91[EUR][1000 genomes]
rs1052741	0.89[EUR][1000 genomes]
rs10807841	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10951169	0.87[EUR][1000 genomes]
rs10951171	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10951172	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10951175	0.81[EUR][1000 genomes]
rs1111647	0.87[EUR][1000 genomes]
rs1115347	0.81[EUR][1000 genomes]
rs11762342	0.82[EUR][1000 genomes]
rs11763449	0.82[EUR][1000 genomes]
rs11767188	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12537499	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12665991	0.82[EUR][1000 genomes]
rs12667235	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12667610	0.82[EUR][1000 genomes]
rs12668430	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12670415	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12670771	0.82[EUR][1000 genomes]
rs12700817	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12700819	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12700822	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13226102	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13308974	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1404276	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1404278	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1524532	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1524533	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1554641	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1608664	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1851913	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1880370	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1980329	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2037638	0.82[AMR][1000 genomes]
rs2041714	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2080245	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2080246	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2091171	0.88[EUR][1000 genomes]
rs2098315	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2098316	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2110526	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2110528	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2391443	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28416309	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28429439	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3847001	0.89[EUR][1000 genomes]
rs3925338	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4140899	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4348389	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4719898	0.90[EUR][1000 genomes]
rs4719899	0.84[EUR][1000 genomes]
rs4719900	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4719902	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4722719	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4722724	0.84[EUR][1000 genomes]
rs56024263	0.84[EUR][1000 genomes]
rs6462026	0.90[EUR][1000 genomes]
rs6462029	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6462031	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6462034	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6462036	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6462037	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6462038	0.82[EUR][1000 genomes]
rs6947731	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6948814	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6949496	0.89[EUR][1000 genomes]
rs6955074	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6957674	0.88[EUR][1000 genomes]
rs6958467	0.80[EUR][1000 genomes]
rs6959126	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6960834	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6963585	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6970104	0.82[EUR][1000 genomes]
rs6974052	0.87[EUR][1000 genomes]
rs6974387	0.82[EUR][1000 genomes]
rs6980382	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs759269	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7780431	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7783447	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7789788	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7790498	0.84[EUR][1000 genomes]
rs7806605	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7806812	0.82[EUR][1000 genomes]
rs7811436	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9639552	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9639553	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9639560	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs978447	0.83[AMR][1000 genomes];0.92[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	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
rs12539707	HIBADH	Cis_1M	lymphoblastoid	RTeQTL
rs12539707	HIBADH	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27559400-27627800	Weak transcription	Psoas Muscle	Psoas
2	chr7:27582400-27650800	Weak transcription	Left Ventricle	heart
3	chr7:27600600-27645600	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:27603000-27626400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:27603200-27631800	Weak transcription	Primary T cells from cord blood	blood
6	chr7:27603600-27626400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr7:27605800-27645800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:27609400-27632600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:27609400-27651000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:27615600-27626400	Weak transcription	Ovary	ovary
11	chr7:27615600-27626400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr7:27615600-27657800	Weak transcription	Aorta	Aorta
13	chr7:27616000-27626600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr7:27616000-27631600	Weak transcription	Adipose Nuclei	Adipose
15	chr7:27616000-27632800	Weak transcription	HUVEC	blood vessel
16	chr7:27616000-27643400	Weak transcription	Fetal Lung	lung
17	chr7:27616000-27650800	Weak transcription	Fetal Kidney	kidney
18	chr7:27617600-27633000	Weak transcription	A549	lung
19	chr7:27618400-27645000	Weak transcription	Fetal Intestine Large	intestine
20	chr7:27619600-27634800	Weak transcription	Fetal Intestine Small	intestine
21	chr7:27619600-27635600	Weak transcription	Liver	Liver
22	chr7:27619800-27639800	Weak transcription	HepG2	liver
23	chr7:27619800-27643400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:27621000-27626200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:27621000-27626400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr7:27621200-27626200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:27622600-27626600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr7:27624400-27636600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr7:27624800-27627000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr7:27625200-27642600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:27625400-27626400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:27625600-27627400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:27625800-27626600	Weak transcription	HSMMtube	muscle
34	chr7:27625800-27639600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:27625800-27645200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:27626000-27626200	Enhancers	GM12878-XiMat	blood
37	chr7:27626000-27632800	Weak transcription	Osteobl	bone

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