Variant report

Variant	rs7860020
Chromosome Location	chr9:3313984-3313985
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10429463	0.93[EUR][1000 genomes]
rs12004313	0.83[EUR][1000 genomes]
rs13284120	0.89[ASN][1000 genomes]
rs13296552	0.89[ASN][1000 genomes]
rs16916423	0.85[EUR][1000 genomes]
rs17658724	0.87[EUR][1000 genomes]
rs17658838	0.82[EUR][1000 genomes]
rs17715160	0.83[EUR][1000 genomes]
rs17715317	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17715329	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2274487	0.95[ASN][1000 genomes]
rs2304928	0.90[EUR][1000 genomes]
rs2920363	0.85[EUR][1000 genomes]
rs2920364	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2920366	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920368	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920369	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920370	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920376	0.90[ASN][1000 genomes]
rs2920377	0.89[ASN][1000 genomes]
rs2920378	0.90[ASN][1000 genomes]
rs2920379	0.90[ASN][1000 genomes]
rs2920380	0.90[ASN][1000 genomes]
rs2920381	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2920382	0.89[ASN][1000 genomes]
rs2920383	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2986678	0.86[ASN][1000 genomes]
rs2986679	0.89[ASN][1000 genomes]
rs2986680	0.90[ASN][1000 genomes]
rs2986686	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2986687	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2986688	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2986690	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986691	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2986693	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986694	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986695	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986696	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986697	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986698	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2986699	0.86[ASN][1000 genomes]
rs2986700	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2986701	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2986702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2986703	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2991298	0.81[ASN][1000 genomes]
rs2991300	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2991301	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991302	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2991304	0.95[ASN][1000 genomes]
rs2991305	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991306	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2991307	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991308	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991309	0.89[ASN][1000 genomes]
rs2991310	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991311	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991314	0.90[ASN][1000 genomes]
rs2991315	0.90[ASN][1000 genomes]
rs2991316	0.92[ASN][1000 genomes]
rs2991317	0.89[ASN][1000 genomes]
rs2991318	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991319	0.89[ASN][1000 genomes]
rs2991320	0.87[ASN][1000 genomes]
rs2991321	0.87[ASN][1000 genomes]
rs2991323	0.89[ASN][1000 genomes]
rs3012670	0.87[ASN][1000 genomes]
rs3012672	0.87[ASN][1000 genomes]
rs3012692	0.81[ASN][1000 genomes]
rs3012693	0.87[EUR][1000 genomes]
rs3012694	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012695	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012696	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012697	0.84[ASN][1000 genomes]
rs3012700	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3012701	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3012702	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3012705	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3012706	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3012707	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3012708	0.95[ASN][1000 genomes]
rs3012709	0.95[ASN][1000 genomes]
rs3012710	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3012711	0.95[ASN][1000 genomes]
rs3012712	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3012713	0.85[ASN][1000 genomes]
rs4008965	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41312820	0.80[EUR][1000 genomes]
rs4495486	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57295144	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs576347	0.82[EUR][1000 genomes]
rs58010475	0.88[EUR][1000 genomes]
rs59378342	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs612198	0.83[EUR][1000 genomes]
rs617992	0.83[EUR][1000 genomes]
rs6476395	0.81[EUR][1000 genomes]
rs656686	0.81[EUR][1000 genomes]
rs66573713	0.85[ASN][1000 genomes]
rs7025201	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7025328	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7035429	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7044448	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72699004	0.89[EUR][1000 genomes]
rs72699014	0.89[EUR][1000 genomes]
rs72699023	0.87[EUR][1000 genomes]
rs72699033	0.86[EUR][1000 genomes]
rs72699037	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72699039	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72699050	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72699051	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72699063	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72699067	0.87[ASN][1000 genomes]
rs72699069	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7850653	0.85[ASN][1000 genomes]
rs7850660	0.85[ASN][1000 genomes]
rs7859468	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7861667	0.85[ASN][1000 genomes]
rs7861699	0.85[ASN][1000 genomes]
rs7868041	0.81[EUR][1000 genomes]
rs7871277	0.85[ASN][1000 genomes]
rs9408234	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 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	chr9:3265600-3332000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr9:3277400-3337400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr9:3288600-3318800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:3291400-3338600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr9:3291800-3318800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr9:3293200-3329600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:3293400-3318800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr9:3293600-3352600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:3294800-3321200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:3300200-3320000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr9:3302400-3323600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:3305400-3328600	Weak transcription	GM12878-XiMat	blood
15	chr9:3306800-3337400	Weak transcription	Left Ventricle	heart
16	chr9:3307200-3325000	Weak transcription	Pancreas	Pancrea
17	chr9:3308600-3337000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:3309400-3350400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:3309600-3319000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:3310200-3337000	Weak transcription	Primary B cells from cord blood	blood
21	chr9:3311000-3314400	Weak transcription	Fetal Stomach	stomach
22	chr9:3311600-3338800	Weak transcription	Thymus	Thymus
23	chr9:3313200-3337000	Weak transcription	Aorta	Aorta
24	chr9:3313400-3352400	Weak transcription	Primary T cells from cord blood	blood

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