Variant report

Variant	rs58910647
Chromosome Location	chr3:142339050-142339051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:142339008-142339073	Lung_OC	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142337305..142339939-chr3:142351079..142353328,2	K562	blood:
2	chr3:142336507..142339486-chr3:142355322..142357574,2	MCF-7	breast:
3	chr3:142338028..142339583-chr3:142381758..142384613,2	MCF-7	breast:
4	chr3:142336924..142339246-chr3:142443118..142445487,2	MCF-7	breast:

Variant related genes	Relation type
PLS1	TF binding region
ENSG00000144935	Chromatin interaction
ENSG00000120756	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11711434	0.84[ASN][1000 genomes]
rs13316756	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17623058	0.85[ASN][1000 genomes]
rs2140433	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140434	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177397	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28378300	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28647471	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28709617	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4398471	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4582093	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56161530	0.84[ASN][1000 genomes]
rs56383228	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440095	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440096	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440097	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773213	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6797237	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6797745	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6800573	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73228757	0.82[ASN][1000 genomes]
rs73228758	0.82[ASN][1000 genomes]
rs73228762	0.82[ASN][1000 genomes]
rs73228782	0.85[ASN][1000 genomes]
rs73240328	0.86[ASN][1000 genomes]
rs7622648	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7633021	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7638338	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7647212	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7647497	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9683274	0.90[ASN][1000 genomes]
rs9813377	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9816128	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9816275	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9826463	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847445	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857567	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858204	0.86[ASN][1000 genomes]
rs9862686	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868309	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142334000-142357200	Weak transcription	Pancreas	Pancrea
2	chr3:142336000-142339400	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr3:142336000-142340800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr3:142337600-142340600	Weak transcription	Small Intestine	intestine
5	chr3:142337800-142348400	Weak transcription	Gastric	stomach
6	chr3:142338000-142339800	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr3:142338000-142340600	Weak transcription	Fetal Intestine Large	intestine
8	chr3:142338000-142340600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:142338000-142340800	Enhancers	Stomach Mucosa	stomach
10	chr3:142338000-142344200	Weak transcription	Colonic Mucosa	Colon
11	chr3:142338400-142339400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:142338400-142340600	Weak transcription	Fetal Intestine Small	intestine
13	chr3:142338400-142341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:142338600-142343800	Weak transcription	HSMMtube	muscle
15	chr3:142338800-142340200	Enhancers	A549	lung

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