Variant report

Variant	rs2140433
Chromosome Location	chr3:142343691-142343692
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142296526..142298782-chr3:142343605..142345141,2	MCF-7	breast:
2	chr3:142343680..142345636-chr3:142364474..142366774,2	K562	blood:

Variant related genes	Relation type
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11711434	0.84[ASN][1000 genomes]
rs13316756	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17623058	0.85[ASN][1000 genomes]
rs2140434	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28378300	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28647471	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28709617	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821647	0.85[CEU][hapmap]
rs4259003	0.85[CEU][hapmap]
rs4398471	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4582093	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56161530	0.84[ASN][1000 genomes]
rs56383228	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58910647	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440095	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440096	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440097	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773213	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6778383	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs6797237	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797745	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[EUR][1000 genomes]
rs6800573	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[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	0.91[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7633021	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7638338	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7647212	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7647497	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9683274	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9813377	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9816128	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9816275	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9826463	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851381	0.84[CEU][hapmap]
rs9857567	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858204	0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9862686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868309	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142334000-142357200	Weak transcription	Pancreas	Pancrea
2	chr3:142337800-142348400	Weak transcription	Gastric	stomach
3	chr3:142338000-142344200	Weak transcription	Colonic Mucosa	Colon
4	chr3:142338600-142343800	Weak transcription	HSMMtube	muscle
5	chr3:142340200-142345600	Weak transcription	A549	lung
6	chr3:142341400-142346200	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr3:142342400-142345200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr3:142342600-142345000	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr3:142342800-142343800	Weak transcription	Fetal Intestine Large	intestine
10	chr3:142342800-142345800	Active TSS	Duodenum Mucosa	Duodenum
11	chr3:142343200-142343800	Enhancers	Fetal Lung	lung
12	chr3:142343400-142348600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:142343400-142366400	Weak transcription	Fetal Intestine Small	intestine
14	chr3:142343600-142345000	Weak transcription	Stomach Mucosa	stomach

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