Variant report

Variant	rs649990
Chromosome Location	chr9:3249239-3249240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10429463	0.91[CEU][hapmap]
rs1147822	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11998979	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12004313	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12004744	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1443205	0.93[CEU][hapmap]
rs16916423	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17658724	0.83[EUR][1000 genomes]
rs17658838	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17715051	0.84[CEU][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs17715160	0.85[CEU][hapmap]
rs17715317	0.92[CEU][hapmap]
rs2920363	0.85[EUR][1000 genomes]
rs2920369	0.84[CEU][hapmap]
rs2920375	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2920381	0.85[CEU][hapmap]
rs2920382	0.90[CEU][hapmap]
rs2986686	0.92[CEU][hapmap]
rs2986687	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2986688	0.88[EUR][1000 genomes]
rs2986690	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2986691	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2986693	0.85[EUR][1000 genomes]
rs2986694	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2986695	0.85[CEU][hapmap]
rs2986696	0.85[CEU][hapmap]
rs2986697	0.91[CEU][hapmap]
rs2986698	0.85[CEU][hapmap]
rs2986700	0.92[CEU][hapmap]
rs2991297	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2991298	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2991300	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2991301	0.92[CEU][hapmap]
rs2991302	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2991305	0.84[CEU][hapmap]
rs2991306	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs2991308	0.92[CEU][hapmap]
rs2991310	0.85[CEU][hapmap]
rs2991311	0.85[CEU][hapmap]
rs2991318	0.85[CEU][hapmap]
rs3012686	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3012688	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3012692	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3012693	1.00[CEU][hapmap]
rs3012694	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs3012695	0.92[CEU][hapmap]
rs3012696	0.83[CEU][hapmap]
rs3012697	0.84[CEU][hapmap]
rs3012700	0.84[CEU][hapmap]
rs3012701	0.85[CEU][hapmap]
rs3012706	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3012710	0.85[CEU][hapmap]
rs3012712	0.83[CEU][hapmap]
rs41312820	0.90[EUR][1000 genomes]
rs472139	0.90[ASN][1000 genomes]
rs474845	0.86[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs490961	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs494348	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs506149	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs527697	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs535305	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs535614	0.85[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs540859	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576347	0.83[EUR][1000 genomes]
rs594370	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs612198	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs617047	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs617992	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs619401	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs625941	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs633893	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs636548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs645583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646529	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs656686	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs658123	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7025201	0.85[CEU][hapmap]
rs7025328	0.92[CEU][hapmap]
rs7035429	0.85[CEU][hapmap]
rs72699004	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72699014	0.81[EUR][1000 genomes]
rs72699023	0.83[EUR][1000 genomes]
rs7850999	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7866129	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7868041	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873658	0.92[ASN][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	nsv1028668	chr9:3139007-3262791	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv539939	chr9:3139007-3262791	Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3220000-3256600	Weak transcription	Brain Anterior Caudate	brain
2	chr9:3220400-3287400	Weak transcription	Psoas Muscle	Psoas
3	chr9:3221800-3251400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:3221800-3256400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:3222200-3256200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:3222200-3269400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr9:3222400-3254800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:3223200-3254800	Weak transcription	Brain Angular Gyrus	brain
9	chr9:3223200-3277000	Weak transcription	HSMMtube	muscle
10	chr9:3223400-3270200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:3223600-3255400	Weak transcription	Right Ventricle	heart
12	chr9:3223600-3256600	Weak transcription	Thymus	Thymus
13	chr9:3223600-3264400	Weak transcription	Fetal Intestine Small	intestine
14	chr9:3223600-3271600	Weak transcription	Lung	lung
15	chr9:3223600-3284800	Weak transcription	Spleen	Spleen
16	chr9:3224000-3275800	Weak transcription	Gastric	stomach
17	chr9:3225200-3262800	Weak transcription	Esophagus	oesophagus
18	chr9:3225800-3255600	Weak transcription	Fetal Stomach	stomach
19	chr9:3226600-3289600	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:3227400-3256600	Weak transcription	Brain Hippocampus Middle	brain
21	chr9:3230000-3254200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr9:3232000-3253200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:3232000-3254600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:3232400-3256400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr9:3233600-3256400	Weak transcription	Brain Substantia Nigra	brain
26	chr9:3233600-3292600	Weak transcription	Pancreas	Pancrea
27	chr9:3234000-3256400	Weak transcription	Liver	Liver
28	chr9:3234800-3294400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr9:3235800-3269800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr9:3236000-3255200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:3236200-3271600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr9:3236800-3254800	Weak transcription	Brain Germinal Matrix	brain
33	chr9:3236800-3254800	Weak transcription	Ovary	ovary
34	chr9:3236800-3256400	Weak transcription	Fetal Brain Female	brain
35	chr9:3236800-3257000	Weak transcription	Aorta	Aorta
36	chr9:3236800-3266600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:3238000-3276800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr9:3238200-3254800	Weak transcription	Fetal Brain Male	brain
39	chr9:3238600-3263800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:3241400-3278000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr9:3241600-3250400	Weak transcription	Fetal Lung	lung
42	chr9:3241600-3254800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:3241600-3276800	Weak transcription	Placenta	Placenta
44	chr9:3241800-3255200	Weak transcription	Fetal Kidney	kidney
45	chr9:3241800-3256400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr9:3241800-3256600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr9:3241800-3271200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:3242000-3254000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr9:3242000-3262400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:3242000-3278000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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