Variant report

Variant	rs3012693
Chromosome Location	chr9:3294797-3294798
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 150 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10429463	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes]
rs1147822	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs11998979	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12004313	0.83[EUR][1000 genomes]
rs12004744	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap]
rs13296552	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1443205	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs16916423	0.87[ASW][hapmap];1.00[CEU][hapmap];0.82[MEX][hapmap];0.88[EUR][1000 genomes]
rs17658724	0.90[EUR][1000 genomes]
rs17658838	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs17715051	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs17715160	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs17715317	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17715329	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2274487	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2304928	0.89[EUR][1000 genomes]
rs2920363	0.84[EUR][1000 genomes]
rs2920364	0.85[ASN][1000 genomes]
rs2920366	0.86[ASN][1000 genomes]
rs2920368	0.86[ASN][1000 genomes]
rs2920369	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920370	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920375	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920376	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2920377	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2920378	1.00[CHB][hapmap]
rs2920379	1.00[CHB][hapmap]
rs2920380	1.00[CHB][hapmap]
rs2920381	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2920382	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs2920383	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2986678	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2986679	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2986680	1.00[CHB][hapmap]
rs2986684	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2986686	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2986687	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2986688	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2986690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2986691	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2986693	0.91[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2986694	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2986695	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2986696	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2986697	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2986698	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2986699	0.86[ASN][1000 genomes]
rs2986700	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986701	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986702	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2986703	0.86[EUR][1000 genomes]
rs2991297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2991300	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2991301	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2991302	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2991304	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2991305	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2991306	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2991307	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2991308	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2991309	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2991310	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2991311	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2991314	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2991315	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2991317	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2991318	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs2991319	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2991320	1.00[CHB][hapmap]
rs2991321	1.00[CHB][hapmap]
rs2991322	1.00[CHB][hapmap]
rs2991323	1.00[CHB][hapmap]
rs3012670	1.00[CHB][hapmap]
rs3012672	1.00[CHB][hapmap]
rs3012686	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs3012688	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs3012692	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs3012694	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3012695	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3012696	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3012697	0.84[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs3012700	0.83[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012701	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012702	0.85[ASN][1000 genomes]
rs3012705	0.82[EUR][1000 genomes]
rs3012706	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap]
rs3012707	0.86[EUR][1000 genomes]
rs3012708	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs3012709	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs3012710	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3012711	1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs3012712	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs3012713	1.00[CHB][hapmap]
rs4008965	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41312820	0.84[EUR][1000 genomes]
rs4495486	0.81[ASN][1000 genomes]
rs474845	0.85[CEU][hapmap]
rs490961	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs494348	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs506149	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap]
rs515913	0.82[JPT][hapmap]
rs535614	0.85[CEU][hapmap]
rs57295144	0.88[EUR][1000 genomes]
rs576347	0.86[EUR][1000 genomes]
rs58010475	0.92[EUR][1000 genomes]
rs59378342	0.88[EUR][1000 genomes]
rs594370	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs612198	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs617047	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs617992	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs619401	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap]
rs625941	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs633893	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs636548	1.00[CEU][hapmap];0.91[GIH][hapmap]
rs649990	1.00[CEU][hapmap]
rs656686	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs658123	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs7025201	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7025328	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7035429	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs7044448	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72699004	0.88[EUR][1000 genomes]
rs72699014	0.88[EUR][1000 genomes]
rs72699023	0.90[EUR][1000 genomes]
rs72699033	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72699037	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72699039	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72699041	0.89[ASN][1000 genomes]
rs72699050	0.86[EUR][1000 genomes]
rs72699051	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7850653	0.89[CHB][hapmap]
rs7850660	1.00[CHB][hapmap]
rs7850999	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[EUR][1000 genomes]
rs7855364	1.00[CHB][hapmap]
rs7859468	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7860020	0.87[EUR][1000 genomes]
rs7861667	1.00[CHB][hapmap]
rs7861699	1.00[CHB][hapmap]
rs7868041	0.80[EUR][1000 genomes]
rs7871277	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv466090	chr9:3237378-3349487	Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv613145	chr9:3237378-3349487	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1032529	chr9:3254763-3319778	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv539941	chr9:3254763-3319778	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3244200-3338400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:3263200-3297800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:3265600-3332000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:3272000-3302800	Weak transcription	Ovary	ovary
5	chr9:3275800-3295600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr9:3276600-3295000	Weak transcription	Fetal Thymus	thymus
7	chr9:3276800-3299400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr9:3277400-3310600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:3277400-3337400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:3286600-3296800	Weak transcription	Aorta	Aorta
11	chr9:3286600-3307000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:3287400-3295000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:3287600-3296400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr9:3288000-3305600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:3288200-3294800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:3288200-3294800	Weak transcription	Fetal Intestine Large	intestine
17	chr9:3288200-3296800	Weak transcription	Left Ventricle	heart
18	chr9:3288200-3309000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr9:3288400-3299200	Weak transcription	Primary B cells from cord blood	blood
21	chr9:3288600-3318800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr9:3290200-3299600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr9:3290600-3299200	Weak transcription	GM12878-XiMat	blood
24	chr9:3290800-3309200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:3291000-3294800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:3291000-3296800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:3291000-3299000	Weak transcription	Fetal Brain Male	brain
28	chr9:3291400-3338600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:3291800-3318800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr9:3292000-3300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:3293200-3329600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:3293400-3295200	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr9:3293400-3299800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:3293400-3312800	Weak transcription	Primary T cells from cord blood	blood
35	chr9:3293400-3312800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr9:3293400-3318800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:3293600-3301400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:3293600-3352600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr9:3294600-3299400	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links