Variant report

Variant	rs12194061
Chromosome Location	chr6:109867642-109867643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10457192	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10457194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10457195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10457203	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1046943	0.87[CEU][hapmap]
rs1048203	0.86[CHB][hapmap]
rs10499053	0.90[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1074765	0.87[CEU][hapmap]
rs1074766	0.87[CEU][hapmap]
rs10782162	0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs10782163	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10872034	0.89[ASN][1000 genomes]
rs11153174	0.86[CHB][hapmap]
rs11153175	0.86[CHB][hapmap]
rs11153183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11153188	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153213	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs11153215	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs11251	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs11752791	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11754340	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11754455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11755641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11967108	0.86[CHB][hapmap]
rs12190920	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs12191353	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12192268	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs12192776	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12192847	0.81[ASN][1000 genomes]
rs12193719	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12194157	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12195904	0.85[EUR][1000 genomes]
rs12197114	0.86[CHB][hapmap]
rs12197180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12197838	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12197950	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12198938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12199154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12201356	0.82[EUR][1000 genomes]
rs12201444	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs12204548	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs12205140	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12205485	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12208018	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12208933	0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs12209691	0.81[ASN][1000 genomes]
rs12210706	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12212476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12214639	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12215077	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs12524639	0.86[CHB][hapmap]
rs12528781	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13191066	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13199109	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13199135	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13201430	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs13201947	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13201951	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13203587	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13204102	0.88[ASN][1000 genomes]
rs13204500	0.88[ASN][1000 genomes]
rs1321328	0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs13220915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1322124	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs1358998	0.86[CHB][hapmap]
rs1406899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1476387	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs1476388	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17070591	0.88[CEU][hapmap]
rs1923725	0.86[CHB][hapmap]
rs1960325	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1980591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1998811	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2024849	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2024850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2024852	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2024853	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2025148	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs2148089	0.86[ASN][1000 genomes]
rs2208209	0.92[ASN][1000 genomes]
rs2236084	0.87[CEU][hapmap]
rs2236582	0.86[CHB][hapmap]
rs2273752	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2275650	0.82[CHB][hapmap]
rs2277113	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs2277114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2357124	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2884037	0.88[CEU][hapmap]
rs36131450	0.87[ASN][1000 genomes]
rs3734652	0.87[CEU][hapmap]
rs3757234	0.86[CHB][hapmap]
rs3757235	0.87[CEU][hapmap]
rs3778474	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs3778477	0.80[ASN][1000 genomes]
rs3799842	0.83[CEU][hapmap]
rs3799845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[YRI][hapmap];0.82[EUR][1000 genomes]
rs3799849	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs3807005	0.81[ASN][1000 genomes]
rs3899233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4141930	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs4490694	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945833	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4946967	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs6568592	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68042406	0.89[ASN][1000 genomes]
rs6906216	0.91[ASN][1000 genomes]
rs6911700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6914498	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs6916579	0.90[ASN][1000 genomes]
rs6920292	0.89[ASN][1000 genomes]
rs6920372	0.88[CEU][hapmap]
rs6926096	0.91[ASN][1000 genomes]
rs71541003	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs729888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs730089	0.87[CEU][hapmap]
rs7341297	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs736830	0.87[CEU][hapmap]
rs749517	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs752262	0.86[CHB][hapmap]
rs7748669	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs7754650	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs7755941	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7767525	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7768973	0.88[CEU][hapmap]
rs7773095	0.86[CHB][hapmap]
rs7773950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910730	0.91[CEU][hapmap];0.81[JPT][hapmap]
rs9480947	0.88[CEU][hapmap]
rs9480948	0.86[CHB][hapmap]
rs9480956	0.88[CEU][hapmap]
rs9480957	0.86[CHB][hapmap]
rs9487070	0.88[CEU][hapmap]
rs9487100	0.86[CHB][hapmap]
rs9487103	0.87[CEU][hapmap]
rs971434	0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs974034	0.87[CEU][hapmap]
rs9791241	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026012	chr6:109851638-109999379	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv604484	chr6:109851937-109997529	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12194061	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12194061	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs12194061	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12194061	SMPD2	cis	Whole Blood	GTEx
rs12194061	RP11-425D10.10	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109848400-109870400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:109850800-109870000	Weak transcription	Left Ventricle	heart
3	chr6:109852200-109878400	Weak transcription	Pancreas	Pancrea
4	chr6:109859200-109868000	Weak transcription	Spleen	Spleen
5	chr6:109859200-109873000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:109860200-109870000	Weak transcription	Adipose Nuclei	Adipose
7	chr6:109860600-109870000	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:109861200-109870200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:109862200-109869600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:109862200-109869600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:109862200-109870000	Weak transcription	Primary B cells from cord blood	blood
12	chr6:109862200-109878200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:109862200-109878400	Weak transcription	Thymus	Thymus
14	chr6:109863000-109870000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:109863600-109867800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:109864200-109870200	Weak transcription	Brain Anterior Caudate	brain
17	chr6:109864200-109870200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:109865400-109870000	Weak transcription	Liver	Liver
19	chr6:109865800-109869000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:109866400-109870200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:109867000-109869600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:109867000-109885800	Weak transcription	Ovary	ovary
23	chr6:109867400-109869600	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links