Variant report

Variant	rs2080246
Chromosome Location	chr7:27569704-27569705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 154 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs1005128	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1009252	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1014373	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1015265	0.86[AMR][1000 genomes]
rs1015750	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1030003	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10447552	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1052724	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052741	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807841	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951169	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951171	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951172	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951175	0.84[EUR][1000 genomes]
rs1111647	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1115347	0.81[EUR][1000 genomes]
rs11526176	1.00[ASN][1000 genomes]
rs11762342	0.82[EUR][1000 genomes]
rs11763449	0.82[EUR][1000 genomes]
rs11767188	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973492	0.83[EUR][1000 genomes]
rs12155430	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12535844	0.82[EUR][1000 genomes]
rs12537499	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539707	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12540276	1.00[ASN][1000 genomes]
rs12665991	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12667235	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12667610	0.82[EUR][1000 genomes]
rs12668430	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670415	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12670771	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12672811	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12673949	0.88[AMR][1000 genomes]
rs12700813	1.00[ASN][1000 genomes]
rs12700815	1.00[ASN][1000 genomes]
rs12700817	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700819	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12700822	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13226102	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13227873	1.00[ASN][1000 genomes]
rs13242248	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13244903	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13246464	0.80[AMR][1000 genomes]
rs13308974	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1357760	1.00[ASN][1000 genomes]
rs1404276	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404278	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404282	0.88[AMR][1000 genomes]
rs1524526	0.90[ASN][1000 genomes]
rs1524529	0.88[AMR][1000 genomes]
rs1524530	1.00[ASN][1000 genomes]
rs1524531	1.00[ASN][1000 genomes]
rs1524532	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524533	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554641	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608663	0.88[AMR][1000 genomes]
rs1608664	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851911	0.90[ASN][1000 genomes]
rs1851912	0.90[ASN][1000 genomes]
rs1851913	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880370	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980329	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980330	0.88[AMR][1000 genomes]
rs1986243	1.00[ASN][1000 genomes]
rs2037638	0.87[AMR][1000 genomes]
rs2041714	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041715	0.88[AMR][1000 genomes]
rs2080245	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091171	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098315	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098316	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110526	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110528	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391443	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391444	0.82[AMR][1000 genomes]
rs2391445	0.85[AMR][1000 genomes]
rs2391446	0.85[AMR][1000 genomes]
rs2391449	0.81[EUR][1000 genomes]
rs2391452	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2391453	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28416309	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28429439	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34886410	1.00[ASN][1000 genomes]
rs3847001	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3925338	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4140899	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42085	0.81[AMR][1000 genomes]
rs4348389	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719898	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719899	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4719900	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719902	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722719	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722724	0.84[EUR][1000 genomes]
rs4722728	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56139857	0.83[EUR][1000 genomes]
rs6462026	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462029	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6462031	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462032	1.00[ASN][1000 genomes]
rs6462033	0.88[AMR][1000 genomes]
rs6462034	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6462036	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6462037	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6462038	0.82[EUR][1000 genomes]
rs6945993	0.83[EUR][1000 genomes]
rs6946075	1.00[ASN][1000 genomes]
rs6947731	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948460	0.81[AMR][1000 genomes]
rs6948814	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949496	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955074	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956484	1.00[ASN][1000 genomes]
rs6957674	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958467	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6959126	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6959495	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6960834	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963421	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6963585	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964190	1.00[ASN][1000 genomes]
rs6966587	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6966918	1.00[ASN][1000 genomes]
rs6970104	0.82[EUR][1000 genomes]
rs6974052	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974387	0.82[EUR][1000 genomes]
rs6974932	0.82[EUR][1000 genomes]
rs6980382	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723699	1.00[ASN][1000 genomes]
rs723700	1.00[ASN][1000 genomes]
rs7455882	1.00[ASN][1000 genomes]
rs759269	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759270	0.85[AMR][1000 genomes]
rs759271	0.85[AMR][1000 genomes]
rs7779240	1.00[ASN][1000 genomes]
rs7780431	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783447	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7786973	0.88[AMR][1000 genomes]
rs7789788	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790498	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7794292	0.90[ASN][1000 genomes]
rs7806605	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806812	0.82[EUR][1000 genomes]
rs7811436	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs940525	1.00[ASN][1000 genomes]
rs940526	1.00[ASN][1000 genomes]
rs9639552	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639553	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639559	0.88[AMR][1000 genomes]
rs9639560	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974883	0.88[AMR][1000 genomes]
rs978447	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv830930	chr7:27395838-27587355	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2080246	HIBADH	cis	multi-tissue	Pritchard
rs2080246	HIBADH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27553200-27581000	Weak transcription	Fetal Heart	heart
2	chr7:27555800-27581000	Weak transcription	Gastric	stomach
3	chr7:27556000-27579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:27556000-27581600	Weak transcription	HMEC	breast
5	chr7:27556400-27584400	Weak transcription	NHEK	skin
6	chr7:27556400-27586400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:27557200-27573400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr7:27558000-27579800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:27559400-27584200	Weak transcription	Pancreas	Pancrea
10	chr7:27559400-27627800	Weak transcription	Psoas Muscle	Psoas
11	chr7:27559800-27593000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:27560800-27578800	Weak transcription	NHLF	lung
13	chr7:27561200-27580200	Weak transcription	Colon Smooth Muscle	Colon
14	chr7:27561200-27580600	Strong transcription	Liver	Liver
15	chr7:27561600-27583000	Weak transcription	Colonic Mucosa	Colon
16	chr7:27561800-27580200	Weak transcription	Fetal Stomach	stomach
17	chr7:27562400-27579800	Weak transcription	NH-A	brain
18	chr7:27562400-27581000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:27562400-27581000	Weak transcription	Spleen	Spleen
20	chr7:27563000-27580000	Weak transcription	Fetal Thymus	thymus
21	chr7:27563000-27581000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr7:27563200-27579800	Weak transcription	Brain Angular Gyrus	brain
23	chr7:27563400-27580800	Weak transcription	GM12878-XiMat	blood
24	chr7:27563400-27581800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr7:27563600-27571000	Strong transcription	Primary T cells from cord blood	blood
26	chr7:27563800-27569800	Strong transcription	Dnd41	blood
27	chr7:27563800-27571000	Strong transcription	A549	lung
28	chr7:27563800-27571200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:27564000-27569800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr7:27564000-27571000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr7:27564000-27573200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:27564000-27580800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:27564200-27582000	Weak transcription	Stomach Mucosa	stomach
34	chr7:27564200-27585400	Weak transcription	Small Intestine	intestine
35	chr7:27564400-27571200	Weak transcription	HUVEC	blood vessel
36	chr7:27565200-27571200	Strong transcription	HepG2	liver
37	chr7:27565200-27581600	Weak transcription	Esophagus	oesophagus
38	chr7:27565600-27592200	Weak transcription	Brain Substantia Nigra	brain
39	chr7:27565800-27575800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr7:27566000-27579800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr7:27566000-27580000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr7:27566000-27580000	Weak transcription	Thymus	Thymus
43	chr7:27566000-27580200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:27566000-27580600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:27566000-27581000	Weak transcription	Brain Anterior Caudate	brain
46	chr7:27566000-27583800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr7:27566200-27579800	Weak transcription	Hela-S3	cervix
48	chr7:27566200-27580000	Weak transcription	K562	blood
49	chr7:27566400-27572800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:27566400-27579600	Weak transcription	Primary T cells fromperipheralblood	blood

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