Variant report

Variant	rs12673949
Chromosome Location	chr7:27600634-27600635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs1005128	0.90[AMR][1000 genomes]
rs10081338	0.85[AMR][1000 genomes]
rs10081339	0.85[AMR][1000 genomes]
rs1009252	0.90[AMR][1000 genomes]
rs1014373	0.88[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1015265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1015750	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10224961	0.81[ASN][1000 genomes]
rs10231814	0.88[ASN][1000 genomes]
rs10233212	0.87[ASN][1000 genomes]
rs10240622	0.81[ASN][1000 genomes]
rs10242812	0.81[ASN][1000 genomes]
rs10256159	0.87[YRI][hapmap]
rs1030003	1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs10447552	0.90[MEX][hapmap]
rs10486548	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10499580	0.81[ASN][1000 genomes]
rs1052724	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1052741	0.86[AMR][1000 genomes]
rs10807841	0.91[AMR][1000 genomes]
rs10951171	0.91[AMR][1000 genomes]
rs10951172	0.91[AMR][1000 genomes]
rs10951173	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11764753	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11767188	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12530626	0.81[CEU][hapmap]
rs12531518	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12537499	0.90[MEX][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12540063	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12667235	0.90[MEX][hapmap];0.88[AMR][1000 genomes]
rs12668430	0.90[MEX][hapmap];0.87[AMR][1000 genomes]
rs12670415	0.81[CEU][hapmap];0.91[AMR][1000 genomes]
rs12700817	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12700819	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12700822	0.87[AMR][1000 genomes]
rs12700823	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12700824	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12700825	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12700826	0.81[CEU][hapmap]
rs12700828	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12700829	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12700830	1.00[CEU][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13226102	0.87[AMR][1000 genomes]
rs13308974	0.87[AMR][1000 genomes]
rs1404276	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1404278	0.88[AMR][1000 genomes]
rs1404282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524532	0.91[AMR][1000 genomes]
rs1524533	0.90[AMR][1000 genomes]
rs1554641	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1608663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608664	0.91[AMR][1000 genomes]
rs17136532	0.81[ASN][1000 genomes]
rs17155388	0.81[ASN][1000 genomes]
rs1851913	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1880370	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1980329	0.90[AMR][1000 genomes]
rs1980330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037638	0.81[AMR][1000 genomes]
rs2041714	0.90[MEX][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2041715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080245	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2080246	0.88[AMR][1000 genomes]
rs2091171	0.81[AMR][1000 genomes]
rs2098315	0.91[AMR][1000 genomes]
rs2098316	0.88[AMR][1000 genomes]
rs2110526	0.86[AMR][1000 genomes]
rs2110528	0.87[AMR][1000 genomes]
rs2160125	1.00[CEU][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2391443	0.91[AMR][1000 genomes]
rs2391444	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391445	1.00[CEU][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2391446	1.00[CEU][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2391447	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2391448	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2391451	1.00[CEU][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2391454	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28416309	0.86[AMR][1000 genomes]
rs28429439	0.82[AMR][1000 genomes]
rs3847001	0.86[AMR][1000 genomes]
rs3925338	0.90[MEX][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4140899	0.90[MEX][hapmap];0.91[AMR][1000 genomes]
rs42085	0.80[MEX][hapmap]
rs42087	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes]
rs42088	0.88[YRI][hapmap]
rs42092	0.83[AMR][1000 genomes]
rs4348389	0.91[AMR][1000 genomes]
rs4719898	0.86[AMR][1000 genomes]
rs4719899	0.82[AMR][1000 genomes]
rs4719900	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4719902	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4722719	0.90[MEX][hapmap];0.91[AMR][1000 genomes]
rs4722726	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6462026	0.86[AMR][1000 genomes]
rs6462029	0.91[AMR][1000 genomes]
rs6462031	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6462033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462034	0.86[AMR][1000 genomes]
rs6462036	0.87[AMR][1000 genomes]
rs6462037	0.87[AMR][1000 genomes]
rs6462039	1.00[CEU][hapmap];0.95[MEX][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6943883	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6946305	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6947731	0.88[AMR][1000 genomes]
rs6948814	0.87[AMR][1000 genomes]
rs6949496	0.81[AMR][1000 genomes]
rs6952874	0.81[ASN][1000 genomes]
rs6954905	1.00[CEU][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6955074	0.88[AMR][1000 genomes]
rs6957378	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6957674	0.81[AMR][1000 genomes]
rs6958467	0.82[AMR][1000 genomes]
rs6958747	0.90[MEX][hapmap]
rs6959126	0.90[AMR][1000 genomes]
rs6960834	0.88[AMR][1000 genomes]
rs6963585	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6966091	0.86[CEU][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6974052	0.81[AMR][1000 genomes]
rs6974387	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6974932	0.90[MEX][hapmap]
rs6980308	0.81[ASN][1000 genomes]
rs6980382	0.88[AMR][1000 genomes]
rs759269	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs759270	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs759271	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7779990	0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7780431	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7782422	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7783447	0.91[AMR][1000 genomes]
rs7786973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7789788	0.91[AMR][1000 genomes]
rs7796520	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7806415	1.00[CEU][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7806605	0.90[AMR][1000 genomes]
rs7808275	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7811436	0.87[AMR][1000 genomes]
rs961723	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs961724	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs961725	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9639552	0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9639553	0.91[AMR][1000 genomes]
rs9639559	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639560	0.91[AMR][1000 genomes]
rs974883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978447	0.89[MEX][hapmap];0.91[AMR][1000 genomes];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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12673949	HIBADH	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27559400-27627800	Weak transcription	Psoas Muscle	Psoas
2	chr7:27569600-27602200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:27580600-27615000	Weak transcription	Aorta	Aorta
4	chr7:27581400-27617400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:27581600-27602800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr7:27581800-27603000	Weak transcription	Fetal Lung	lung
7	chr7:27582200-27603000	Weak transcription	Primary T cells from cord blood	blood
8	chr7:27582400-27650800	Weak transcription	Left Ventricle	heart
9	chr7:27582800-27604800	Weak transcription	Fetal Kidney	kidney
10	chr7:27582800-27615000	Weak transcription	Placenta	Placenta
11	chr7:27582800-27615200	Weak transcription	Ovary	ovary
12	chr7:27587400-27602600	Weak transcription	Adipose Nuclei	Adipose
13	chr7:27587800-27602600	Weak transcription	HSMM	muscle
14	chr7:27595800-27603000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:27596000-27602600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:27600200-27601000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:27600200-27601200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr7:27600200-27601200	Enhancers	Osteobl	bone
19	chr7:27600200-27601400	Enhancers	NHDF-Ad	bronchial
20	chr7:27600200-27601600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:27600400-27601000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:27600400-27601000	Strong transcription	Liver	Liver
23	chr7:27600400-27601200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:27600400-27601200	Enhancers	HSMMtube	muscle
25	chr7:27600600-27601000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:27600600-27645600	Weak transcription	Colon Smooth Muscle	Colon

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