Variant report

Variant	rs7861699
Chromosome Location	chr9:3338775-3338776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 142 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10429463	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1147822	0.88[CHB][hapmap]
rs12004744	0.88[CHB][hapmap]
rs12350916	0.92[ASN][1000 genomes]
rs13284120	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13285170	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13296552	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1443205	0.89[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs17658838	0.88[CHB][hapmap]
rs17715160	0.82[CHB][hapmap]
rs17715317	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17715329	0.85[ASN][1000 genomes]
rs2274487	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920364	0.94[ASN][1000 genomes]
rs2920366	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2920368	0.92[ASN][1000 genomes]
rs2920369	1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs2920370	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2920376	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920377	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2920378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[ASN][1000 genomes]
rs2920382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2920383	0.86[ASN][1000 genomes]
rs2986678	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2986679	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2986680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2986684	1.00[CHB][hapmap]
rs2986686	0.89[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2986687	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2986688	0.86[CHB][hapmap]
rs2986690	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2986691	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2986693	0.88[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2986694	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2986695	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2986696	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2986697	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2986698	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2986699	0.89[ASN][1000 genomes]
rs2986700	1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs2986701	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs2986702	0.94[ASN][1000 genomes]
rs2986703	0.85[ASN][1000 genomes]
rs2991297	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2991298	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2991300	1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2991301	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs2991302	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2991304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2991305	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2991306	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2991307	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs2991308	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2991309	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2991310	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs2991311	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs2991314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2991315	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2991316	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2991317	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2991318	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs2991319	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2991320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2991321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2991322	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2991323	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs3012670	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3012672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3012686	0.91[JPT][hapmap]
rs3012688	0.81[JPT][hapmap]
rs3012692	0.89[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs3012693	1.00[CHB][hapmap]
rs3012694	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs3012695	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs3012696	0.88[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs3012697	0.88[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs3012700	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs3012701	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs3012702	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3012705	0.85[ASN][1000 genomes]
rs3012706	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3012707	0.83[ASN][1000 genomes]
rs3012708	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012709	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012710	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs3012711	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[ASN][1000 genomes]
rs3012713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4008965	0.92[ASN][1000 genomes]
rs4495486	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs490961	0.88[CHB][hapmap]
rs494348	0.86[CHB][hapmap]
rs506149	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs57295144	0.85[ASN][1000 genomes]
rs59378342	0.85[ASN][1000 genomes]
rs594370	0.88[CHB][hapmap]
rs617047	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs617992	0.88[CHB][hapmap]
rs619401	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs625941	0.88[CHB][hapmap]
rs633893	0.88[CHB][hapmap]
rs6476395	0.80[ASN][1000 genomes]
rs656686	0.88[CHB][hapmap]
rs658123	0.88[CHB][hapmap]
rs66573713	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025201	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs7025328	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7035429	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs7044448	0.83[ASN][1000 genomes]
rs71506635	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71506636	0.91[ASN][1000 genomes]
rs72699037	0.81[ASN][1000 genomes]
rs72699039	0.83[ASN][1000 genomes]
rs72699041	0.80[ASN][1000 genomes]
rs72699050	0.83[ASN][1000 genomes]
rs72699051	0.86[ASN][1000 genomes]
rs72699063	0.94[ASN][1000 genomes]
rs72699067	0.91[ASN][1000 genomes]
rs72699069	0.91[ASN][1000 genomes]
rs7850653	0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7850660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855364	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7859468	0.92[ASN][1000 genomes]
rs7860020	0.85[ASN][1000 genomes]
rs7861667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9408234	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
7	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
8	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
9	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
12	esv3414498	chr9:3338724-3339206	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:3293600-3352600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:3309400-3350400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:3311600-3338800	Weak transcription	Thymus	Thymus
5	chr9:3313400-3352400	Weak transcription	Primary T cells from cord blood	blood
6	chr9:3319000-3347800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr9:3319800-3353800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr9:3320600-3347200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:3322600-3348800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr9:3323800-3342000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr9:3328400-3344400	Weak transcription	Fetal Lung	lung
12	chr9:3330400-3354200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:3331000-3343600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:3333000-3352600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr9:3337000-3338800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:3337000-3338800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:3337200-3338800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:3337400-3338800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr9:3337400-3338800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:3337400-3338800	Enhancers	NHDF-Ad	bronchial
21	chr9:3337400-3338800	Enhancers	Osteobl	bone
22	chr9:3337800-3341600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:3337800-3342200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:3337800-3343400	Weak transcription	HSMM	muscle
25	chr9:3337800-3352600	Weak transcription	Primary B cells from cord blood	blood
26	chr9:3337800-3388800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr9:3338000-3338800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:3338000-3341800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:3338200-3343200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:3338600-3338800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr9:3338600-3338800	Enhancers	Brain Anterior Caudate	brain

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