Variant report

Variant	rs9853463
Chromosome Location	chr3:119610747-119610748
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119610347..119611160-chr3:119865685..119866515,3	MCF-7	breast:
2	chr3:119610644..119611460-chr3:119814072..119814606,2	K562	blood:
3	chr3:119609509..119613184-chr3:119810237..119814414,6	MCF-7	breast:
4	chr3:119609229..119612218-chr3:119810984..119813598,2	K562	blood:
5	chr3:119605247..119607921-chr3:119609001..119610890,2	MCF-7	breast:
6	chr3:119610691..119611222-chr3:119862737..119863328,2	MCF-7	breast:
7	chr3:119610502..119611380-chr3:119901494..119902513,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1037974	1.00[JPT][hapmap]
rs13314836	0.93[AFR][1000 genomes]
rs13322562	0.87[AFR][1000 genomes]
rs1579030	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1579032	1.00[ASN][1000 genomes]
rs17246730	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17246737	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28821007	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34002644	0.93[AFR][1000 genomes]
rs3732358	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4491944	1.00[JPT][hapmap]
rs57265162	1.00[ASN][1000 genomes]
rs58991487	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60049973	0.93[AFR][1000 genomes]
rs60675046	1.00[ASN][1000 genomes]
rs61091679	1.00[EUR][1000 genomes]
rs6796550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72548703	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73854776	1.00[EUR][1000 genomes]
rs922337	1.00[JPT][hapmap]
rs9812146	1.00[YRI][hapmap]
rs9812149	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834346	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9843795	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9849889	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865193	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9867915	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs9872321	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119562400-119611000	Weak transcription	Fetal Stomach	stomach
3	chr3:119569400-119629400	Weak transcription	Esophagus	oesophagus
4	chr3:119574600-119631600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:119582400-119611000	Weak transcription	Brain Anterior Caudate	brain
6	chr3:119582400-119611000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:119582400-119611000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:119582400-119611000	Weak transcription	HUVEC	blood vessel
9	chr3:119582400-119624000	Weak transcription	Brain Germinal Matrix	brain
10	chr3:119582400-119626600	Weak transcription	Fetal Heart	heart
11	chr3:119582400-119629400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:119582600-119611000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:119582600-119611000	Weak transcription	NHLF	lung
14	chr3:119582600-119627200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:119582600-119627400	Weak transcription	Right Ventricle	heart
16	chr3:119582800-119621200	Weak transcription	Fetal Intestine Large	intestine
17	chr3:119583000-119611000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:119583600-119621400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:119583800-119630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:119584000-119622800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:119592600-119617800	Weak transcription	Osteobl	bone
22	chr3:119594800-119610800	Weak transcription	Stomach Mucosa	stomach
23	chr3:119597600-119659000	Weak transcription	Gastric	stomach
24	chr3:119599800-119611000	Weak transcription	Fetal Kidney	kidney
25	chr3:119599800-119611000	Weak transcription	NH-A	brain
26	chr3:119600000-119610800	Weak transcription	Fetal Brain Male	brain
27	chr3:119600000-119611000	Weak transcription	Adipose Nuclei	Adipose
28	chr3:119601000-119611000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:119603200-119611000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:119603200-119611000	Weak transcription	HMEC	breast
31	chr3:119603400-119611000	Weak transcription	HSMMtube	muscle
32	chr3:119603400-119614600	Weak transcription	NHEK	skin
33	chr3:119603400-119624200	Weak transcription	Hela-S3	cervix
34	chr3:119603600-119624200	Weak transcription	HepG2	liver
35	chr3:119604800-119627800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:119607000-119611000	Weak transcription	A549	lung
37	chr3:119608000-119611000	Weak transcription	Aorta	Aorta
38	chr3:119608000-119621600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:119608000-119627800	Weak transcription	Left Ventricle	heart
40	chr3:119608000-119643600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:119608200-119611000	Weak transcription	Fetal Intestine Small	intestine
42	chr3:119608200-119611000	Weak transcription	Ovary	ovary
43	chr3:119608200-119613800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:119608200-119617800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:119608200-119621200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:119608200-119621400	Weak transcription	Placenta	Placenta
47	chr3:119608200-119627400	Weak transcription	Thymus	Thymus
48	chr3:119608200-119639200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:119608400-119610800	Weak transcription	Fetal Lung	lung

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