Variant report

Variant	rs495665
Chromosome Location	chr9:3225608-3225609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2695521..2698232-chr9:3222806..3225730,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12335835	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12683269	0.82[CHB][hapmap]
rs1300076	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16915985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16916092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16916153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16916157	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473778	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs479166	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493667	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs501805	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505371	1.00[ASN][1000 genomes]
rs528224	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531269	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs536485	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs552713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559746	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs577389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598780	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs613518	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs620745	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628884	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629275	1.00[CHB][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs633572	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633614	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs636595	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637109	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs653080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022295	1.00[JPT][hapmap]
rs72697067	1.00[ASN][1000 genomes]
rs72697070	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72697076	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72697078	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72697096	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856125	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7868321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs832297	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs832307	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs866220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1017474	chr9:3019068-3247215	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3212000-3241000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr9:3217200-3245200	Weak transcription	Left Ventricle	heart
3	chr9:3217400-3226800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:3218400-3233200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr9:3218400-3235000	Weak transcription	Primary B cells from cord blood	blood
6	chr9:3220000-3256600	Weak transcription	Brain Anterior Caudate	brain
7	chr9:3220400-3287400	Weak transcription	Psoas Muscle	Psoas
8	chr9:3221200-3240800	Weak transcription	Fetal Kidney	kidney
9	chr9:3221400-3240800	Weak transcription	GM12878-XiMat	blood
10	chr9:3221600-3231000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:3221600-3238600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:3221800-3227600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr9:3221800-3236400	Weak transcription	Fetal Brain Female	brain
14	chr9:3221800-3251400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:3221800-3256400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:3222000-3237600	Weak transcription	NHLF	lung
17	chr9:3222000-3243800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr9:3222000-3246400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:3222000-3247800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr9:3222200-3235200	Weak transcription	Ovary	ovary
21	chr9:3222200-3244400	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:3222200-3244400	Weak transcription	Fetal Thymus	thymus
23	chr9:3222200-3256200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:3222200-3269400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr9:3222400-3235200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr9:3222400-3247400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr9:3222400-3254800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr9:3222600-3226800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr9:3222600-3227000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:3223200-3246400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:3223200-3254800	Weak transcription	Brain Angular Gyrus	brain
32	chr9:3223200-3277000	Weak transcription	HSMMtube	muscle
33	chr9:3223400-3246000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr9:3223400-3270200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:3223600-3233000	Weak transcription	Pancreas	Pancrea
36	chr9:3223600-3243800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr9:3223600-3246400	Weak transcription	Fetal Intestine Large	intestine
38	chr9:3223600-3247800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr9:3223600-3255400	Weak transcription	Right Ventricle	heart
40	chr9:3223600-3256600	Weak transcription	Thymus	Thymus
41	chr9:3223600-3264400	Weak transcription	Fetal Intestine Small	intestine
42	chr9:3223600-3271600	Weak transcription	Lung	lung
43	chr9:3223600-3284800	Weak transcription	Spleen	Spleen
44	chr9:3224000-3236400	Weak transcription	Fetal Lung	lung
45	chr9:3224000-3275800	Weak transcription	Gastric	stomach
46	chr9:3224400-3226000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr9:3224600-3226600	Weak transcription	Brain Hippocampus Middle	brain
48	chr9:3225000-3225800	Enhancers	Fetal Stomach	stomach
49	chr9:3225000-3225800	Enhancers	Rectal Smooth Muscle	rectum
50	chr9:3225200-3226600	Enhancers	Colon Smooth Muscle	Colon

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