Variant report

Variant	rs3012688
Chromosome Location	chr9:3283313-3283314
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 140 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10429463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1147822	1.00[CEU][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11998979	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12004313	0.89[EUR][1000 genomes]
rs12004744	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13296552	0.91[JPT][hapmap]
rs1443205	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16916423	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17658724	0.85[EUR][1000 genomes]
rs17658838	1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17715051	0.84[CEU][hapmap]
rs17715160	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs17715317	0.92[CEU][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs17715329	0.83[EUR][1000 genomes]
rs2274487	0.90[JPT][hapmap]
rs2304928	0.84[EUR][1000 genomes]
rs2920363	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2920368	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2920369	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2920370	0.83[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2920375	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2920376	0.90[JPT][hapmap]
rs2920377	0.91[JPT][hapmap]
rs2920378	0.81[JPT][hapmap]
rs2920379	0.81[JPT][hapmap]
rs2920380	0.81[JPT][hapmap]
rs2920381	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs2920382	0.90[CEU][hapmap]
rs2920383	0.82[EUR][1000 genomes]
rs2986678	0.91[JPT][hapmap]
rs2986679	0.91[JPT][hapmap]
rs2986680	0.81[JPT][hapmap]
rs2986684	0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs2986686	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2986687	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs2986688	1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2986690	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2986691	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2986693	0.91[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2986694	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2986695	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2986696	0.92[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2986697	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2986698	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2986700	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2986701	1.00[JPT][hapmap]
rs2991297	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2991298	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2991300	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2991301	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs2991302	0.92[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs2991304	1.00[JPT][hapmap];0.94[MEX][hapmap]
rs2991305	0.91[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2991306	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2991307	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2991308	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs2991309	1.00[JPT][hapmap]
rs2991310	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs2991311	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs2991314	0.90[JPT][hapmap]
rs2991315	0.90[JPT][hapmap]
rs2991317	0.91[JPT][hapmap]
rs2991318	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs2991319	0.91[JPT][hapmap]
rs2991320	0.81[JPT][hapmap]
rs2991321	0.81[JPT][hapmap]
rs2991322	0.81[JPT][hapmap]
rs3012670	0.81[JPT][hapmap]
rs3012672	0.81[JPT][hapmap]
rs3012680	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3012686	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3012692	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3012693	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs3012694	0.92[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3012695	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs3012696	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3012697	0.87[ASW][hapmap];0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3012700	0.83[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs3012701	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs3012705	0.82[EUR][1000 genomes]
rs3012706	0.87[ASW][hapmap];0.92[CEU][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3012708	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs3012709	1.00[JPT][hapmap]
rs3012710	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs3012711	0.90[JPT][hapmap]
rs3012712	0.91[CEU][hapmap]
rs3012713	0.81[JPT][hapmap]
rs41312820	0.90[EUR][1000 genomes]
rs4495486	0.81[EUR][1000 genomes]
rs474845	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs490961	1.00[CEU][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs494348	0.92[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs506149	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs515913	0.91[JPT][hapmap]
rs527697	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs535305	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs535614	0.85[CEU][hapmap]
rs540859	0.84[EUR][1000 genomes]
rs57295144	0.81[EUR][1000 genomes]
rs576347	0.85[EUR][1000 genomes]
rs58010475	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59378342	0.81[EUR][1000 genomes]
rs594370	1.00[CEU][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs612198	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs617047	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs617992	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs619401	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs625941	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs633893	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs636548	1.00[CEU][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs645583	0.89[EUR][1000 genomes]
rs646529	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6476395	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs649990	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs656686	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs658123	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7025201	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs7025328	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7035429	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs7044448	0.85[EUR][1000 genomes]
rs72699004	0.83[EUR][1000 genomes]
rs72699014	0.83[EUR][1000 genomes]
rs72699023	0.85[EUR][1000 genomes]
rs72699033	0.84[EUR][1000 genomes]
rs72699037	0.82[EUR][1000 genomes]
rs72699039	0.85[EUR][1000 genomes]
rs72699051	0.82[EUR][1000 genomes]
rs7850660	0.81[JPT][hapmap]
rs7850999	1.00[CEU][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs7855364	0.81[JPT][hapmap]
rs7861699	0.81[JPT][hapmap]
rs7866129	0.91[EUR][1000 genomes]
rs7868041	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3220400-3287400	Weak transcription	Psoas Muscle	Psoas
2	chr9:3223600-3284800	Weak transcription	Spleen	Spleen
3	chr9:3226600-3289600	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:3233600-3292600	Weak transcription	Pancreas	Pancrea
5	chr9:3234800-3294400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr9:3242200-3287800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:3244200-3338400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:3246800-3287000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:3251600-3292600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:3254200-3285600	Weak transcription	Fetal Heart	heart
11	chr9:3255000-3293000	Weak transcription	Small Intestine	intestine
12	chr9:3255800-3292800	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:3256800-3293400	Weak transcription	Right Ventricle	heart
14	chr9:3257000-3289000	Weak transcription	Fetal Brain Male	brain
15	chr9:3257200-3290200	Weak transcription	Brain Germinal Matrix	brain
16	chr9:3257200-3290200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:3257200-3290200	Weak transcription	Brain Substantia Nigra	brain
18	chr9:3257200-3294000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:3257200-3294400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr9:3257400-3289000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr9:3257800-3285800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:3263000-3286800	Weak transcription	Liver	Liver
23	chr9:3263200-3294200	Weak transcription	Fetal Lung	lung
24	chr9:3263200-3294600	Weak transcription	Esophagus	oesophagus
25	chr9:3263200-3297800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:3263800-3286600	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:3265200-3291000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:3265400-3287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr9:3265400-3293000	Weak transcription	Brain Angular Gyrus	brain
30	chr9:3265600-3292600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr9:3265600-3332000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr9:3268600-3292000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr9:3270400-3287600	Weak transcription	Adipose Nuclei	Adipose
34	chr9:3270800-3292600	Weak transcription	Brain Anterior Caudate	brain
35	chr9:3271000-3289200	Weak transcription	Thymus	Thymus
36	chr9:3271000-3289600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr9:3271400-3287200	Weak transcription	Left Ventricle	heart
38	chr9:3272000-3291000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:3272000-3292800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:3272000-3302800	Weak transcription	Ovary	ovary
41	chr9:3272600-3288600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr9:3272800-3287400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr9:3274600-3287800	Weak transcription	Fetal Intestine Large	intestine
44	chr9:3275200-3286600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr9:3275600-3286600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr9:3275600-3288800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr9:3275800-3286000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:3275800-3287000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:3275800-3294600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:3275800-3295600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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