Variant report

Variant	rs12116970
Chromosome Location	chr1:150466925-150466926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 197 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:195)

rs_ID	r²[population]
rs1011546	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1043293	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10788874	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10888581	0.95[EUR][1000 genomes]
rs10888582	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs11205366	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11205368	0.93[EUR][1000 genomes]
rs11205369	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11205376	0.96[EUR][1000 genomes]
rs11205378	0.96[EUR][1000 genomes]
rs11205380	0.96[EUR][1000 genomes]
rs11205381	0.96[EUR][1000 genomes]
rs11205383	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11580810	0.95[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs11581051	0.95[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs11582170	0.95[EUR][1000 genomes]
rs11584488	0.92[EUR][1000 genomes]
rs11588184	0.90[EUR][1000 genomes]
rs11588185	0.93[EUR][1000 genomes]
rs11588874	0.99[EUR][1000 genomes]
rs11589873	0.92[EUR][1000 genomes]
rs11808242	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11810419	0.88[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap]
rs11811159	0.99[EUR][1000 genomes]
rs11811950	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12097596	0.85[CHD][hapmap]
rs12120775	0.96[EUR][1000 genomes]
rs12120779	0.96[EUR][1000 genomes]
rs12121133	0.96[EUR][1000 genomes]
rs12121966	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12123103	0.96[EUR][1000 genomes]
rs12126130	0.96[EUR][1000 genomes]
rs12126240	0.96[EUR][1000 genomes]
rs12126327	0.96[EUR][1000 genomes]
rs12126357	0.96[EUR][1000 genomes]
rs12126958	1.00[CEU][hapmap]
rs12128653	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12129037	0.90[ASN][1000 genomes]
rs12129491	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12130082	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12130583	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12131083	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12131672	0.96[EUR][1000 genomes]
rs12132890	0.98[EUR][1000 genomes]
rs12134306	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12136332	0.80[EUR][1000 genomes]
rs12136802	0.99[EUR][1000 genomes]
rs12137967	0.81[EUR][1000 genomes]
rs12139488	0.91[EUR][1000 genomes]
rs12140697	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12141218	0.99[EUR][1000 genomes]
rs12142196	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12144091	0.93[EUR][1000 genomes]
rs12145082	0.99[EUR][1000 genomes]
rs12145566	0.95[EUR][1000 genomes]
rs12145967	0.93[EUR][1000 genomes]
rs12718416	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12726415	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs12729719	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729727	0.94[EUR][1000 genomes]
rs12731738	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12737757	0.99[EUR][1000 genomes]
rs12738490	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs12739019	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12741448	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12745446	0.93[EUR][1000 genomes]
rs12757823	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13057	0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs1343965	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs16830437	0.81[ASN][1000 genomes]
rs16835699	0.81[ASN][1000 genomes]
rs16835708	0.81[ASN][1000 genomes]
rs16835782	0.81[ASN][1000 genomes]
rs16835791	0.81[ASN][1000 genomes]
rs16835911	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16836130	0.85[ASN][1000 genomes]
rs16836139	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16836143	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16836230	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs16836442	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16836576	0.90[ASN][1000 genomes]
rs16836594	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16836601	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16836786	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16836940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16836943	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1694386	0.83[JPT][hapmap]
rs17599629	0.83[JPT][hapmap]
rs1962480	0.96[EUR][1000 genomes]
rs2015966	0.85[ASN][1000 genomes]
rs2173376	0.88[EUR][1000 genomes]
rs2275245	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2275779	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34029237	0.97[EUR][1000 genomes]
rs34247601	0.93[EUR][1000 genomes]
rs34353365	0.88[EUR][1000 genomes]
rs34456572	0.95[EUR][1000 genomes]
rs34906632	0.95[EUR][1000 genomes]
rs34933405	0.96[EUR][1000 genomes]
rs35322831	0.95[EUR][1000 genomes]
rs35591746	0.99[EUR][1000 genomes]
rs35699789	0.94[EUR][1000 genomes]
rs35839589	0.88[EUR][1000 genomes]
rs35989785	0.96[EUR][1000 genomes]
rs36020363	0.99[EUR][1000 genomes]
rs36023386	0.81[EUR][1000 genomes]
rs36029278	0.92[EUR][1000 genomes]
rs36038795	0.93[EUR][1000 genomes]
rs36122812	0.92[EUR][1000 genomes]
rs3737319	0.85[ASN][1000 genomes]
rs3806389	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3850841	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs3850843	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3862206	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs41264059	0.99[EUR][1000 genomes]
rs41264139	0.99[EUR][1000 genomes]
rs4926420	0.85[ASN][1000 genomes]
rs4926421	1.00[JPT][hapmap]
rs4926430	0.94[ASN][1000 genomes]
rs4970925	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4970927	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4970946	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970947	0.96[ASN][1000 genomes]
rs4971044	1.00[CHB][hapmap]
rs522068	0.88[ASN][1000 genomes]
rs55816515	0.98[EUR][1000 genomes]
rs56321241	0.93[EUR][1000 genomes]
rs56882505	0.90[ASN][1000 genomes]
rs56909494	0.90[ASN][1000 genomes]
rs57163995	0.85[ASN][1000 genomes]
rs57272513	0.90[ASN][1000 genomes]
rs57361164	0.81[ASN][1000 genomes]
rs57971032	0.90[ASN][1000 genomes]
rs58419446	0.88[ASN][1000 genomes]
rs58516261	0.85[ASN][1000 genomes]
rs59367061	0.90[ASN][1000 genomes]
rs59378360	0.94[ASN][1000 genomes]
rs59639798	0.90[ASN][1000 genomes]
rs59662772	0.90[ASN][1000 genomes]
rs60459288	0.90[ASN][1000 genomes]
rs60531845	0.85[ASN][1000 genomes]
rs60730811	0.85[ASN][1000 genomes]
rs60758881	0.84[ASN][1000 genomes]
rs66513313	0.98[EUR][1000 genomes]
rs6663989	0.81[JPT][hapmap]
rs6679726	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6680391	0.90[ASN][1000 genomes]
rs6686690	0.93[EUR][1000 genomes]
rs6686809	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6694168	0.96[EUR][1000 genomes]
rs6694394	0.91[EUR][1000 genomes]
rs6700009	0.85[ASN][1000 genomes]
rs6700607	0.82[ASN][1000 genomes]
rs6703798	0.94[EUR][1000 genomes]
rs67566205	0.95[EUR][1000 genomes]
rs67654647	0.95[EUR][1000 genomes]
rs67733549	0.81[EUR][1000 genomes]
rs67903303	0.98[EUR][1000 genomes]
rs68097764	0.90[EUR][1000 genomes]
rs71622690	0.85[ASN][1000 genomes]
rs71622700	0.96[EUR][1000 genomes]
rs72696844	0.83[EUR][1000 genomes]
rs72696853	0.92[EUR][1000 genomes]
rs72698829	0.98[EUR][1000 genomes]
rs72698868	0.99[EUR][1000 genomes]
rs72698870	0.99[EUR][1000 genomes]
rs73011384	0.81[ASN][1000 genomes]
rs73011400	0.81[ASN][1000 genomes]
rs73013119	0.81[ASN][1000 genomes]
rs73013129	0.85[ASN][1000 genomes]
rs73015063	0.85[ASN][1000 genomes]
rs73015078	0.85[ASN][1000 genomes]
rs73015081	0.85[ASN][1000 genomes]
rs73015095	0.85[ASN][1000 genomes]
rs73015096	0.85[ASN][1000 genomes]
rs73017006	0.85[ASN][1000 genomes]
rs73017073	0.90[ASN][1000 genomes]
rs73017086	0.90[ASN][1000 genomes]
rs73017092	0.94[ASN][1000 genomes]
rs73017102	0.90[ASN][1000 genomes]
rs73019017	0.90[ASN][1000 genomes]
rs73019018	0.90[ASN][1000 genomes]
rs73019020	0.90[ASN][1000 genomes]
rs73019021	0.90[ASN][1000 genomes]
rs73019027	0.90[ASN][1000 genomes]
rs73019028	0.90[ASN][1000 genomes]
rs74127616	0.99[EUR][1000 genomes]
rs7417465	0.98[EUR][1000 genomes]
rs7519691	0.81[EUR][1000 genomes]
rs7522820	0.81[EUR][1000 genomes]
rs7542068	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7552883	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs871527	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs953127	0.96[ASN][1000 genomes]
rs9651184	1.00[CEU][hapmap];0.93[EUR][1000 genomes]

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	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
2	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12116970	POLR3GL	cis	cerebellum	SCAN
rs12116970	MRPS21	cis	parietal	SCAN
rs12116970	CTSS	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150460600-150469000	Weak transcription	Pancreas	Pancrea
2	chr1:150460600-150480200	Weak transcription	Right Atrium	heart
3	chr1:150460600-150480200	Weak transcription	Stomach Mucosa	stomach
4	chr1:150460800-150468600	Weak transcription	NHDF-Ad	bronchial
5	chr1:150460800-150470000	Weak transcription	HMEC	breast
6	chr1:150460800-150470600	Weak transcription	Fetal Brain Male	brain
7	chr1:150460800-150476800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:150460800-150478000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:150460800-150480000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:150461000-150486800	Weak transcription	Fetal Heart	heart
11	chr1:150461200-150473600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:150461200-150478200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:150461200-150478600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:150461400-150467000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:150461400-150467000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:150461400-150467000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:150461400-150467000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:150461400-150467000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:150461400-150467000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:150461400-150467000	Strong transcription	Fetal Thymus	thymus
21	chr1:150461400-150467000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:150461400-150467200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:150461400-150467200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:150461400-150467200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:150461400-150467400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:150461400-150470800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:150461400-150475800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:150461400-150480000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:150461400-150480400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:150461400-150480400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:150461400-150480600	Strong transcription	Fetal Intestine Large	intestine
32	chr1:150461600-150467000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr1:150461600-150467000	Strong transcription	Liver	Liver
34	chr1:150461600-150467000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr1:150461600-150467400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:150461600-150467600	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:150461600-150473000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:150461600-150473800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:150461800-150467000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:150461800-150467000	Strong transcription	Fetal Lung	lung
41	chr1:150461800-150473800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:150462000-150468600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:150462000-150480000	Strong transcription	Fetal Stomach	stomach
44	chr1:150462000-150480600	Strong transcription	Fetal Intestine Small	intestine
45	chr1:150462000-150485800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:150462200-150467000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:150462400-150473800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:150462800-150467200	Strong transcription	Fetal Brain Female	brain
49	chr1:150462800-150467200	Strong transcription	Spleen	Spleen
50	chr1:150463000-150467000	Strong transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links