Variant report

Variant	rs6855458
Chromosome Location	chr4:79610032-79610033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79608933..79617994-chr4:79691426..79702696,23	K562	blood:
2	chr4:79602819..79606934-chr4:79608237..79614104,8	K562	blood:
3	chr4:79573896..79576451-chr4:79609109..79611530,2	K562	blood:
4	chr4:79603191..79606883-chr4:79607148..79610716,4	K562	blood:
5	chr4:79609796..79611994-chr4:79696295..79698982,2	MCF-7	breast:
6	chr4:79608764..79617994-chr4:79689698..79699789,21	K562	blood:

Variant related genes	Relation type
ENSG00000138756	Chromatin interaction
ENSG00000260278	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10008008	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10008069	0.87[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10028815	0.82[TSI][hapmap]
rs10029214	0.84[TSI][hapmap]
rs10084949	0.87[EUR][1000 genomes]
rs1134123	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1134124	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931947	0.83[EUR][1000 genomes]
rs13101964	0.84[EUR][1000 genomes]
rs13133277	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1346144	0.91[EUR][1000 genomes]
rs1346145	0.87[ASW][hapmap];0.91[CEU][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1469289	0.87[EUR][1000 genomes]
rs1469290	0.87[EUR][1000 genomes]
rs1582759	0.87[EUR][1000 genomes]
rs1806906	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1834519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1966537	0.86[EUR][1000 genomes]
rs2867465	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867466	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2903578	0.87[EUR][1000 genomes]
rs4074675	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4257676	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4264856	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs4321658	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4365753	0.95[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs4472162	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs4472163	0.82[CEU][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs4495064	0.87[TSI][hapmap]
rs4560439	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4612	0.84[TSI][hapmap]
rs4619914	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6533940	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6815367	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6818230	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6825593	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6842686	0.87[TSI][hapmap]
rs6842723	0.87[TSI][hapmap]
rs7672208	0.89[EUR][1000 genomes]
rs7677162	0.89[EUR][1000 genomes]
rs7694971	0.89[EUR][1000 genomes]
rs7699519	0.89[EUR][1000 genomes]
rs7699905	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9992088	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6855458	LOC643424	cis	multi-tissue	Pritchard
rs6855458	ANXA3	cis	cerebellum	SCAN
rs6855458	CXCL10	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79605800-79612200	Weak transcription	Fetal Intestine Small	intestine
2	chr4:79606000-79610200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:79606000-79611800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:79606600-79612200	Weak transcription	HSMMtube	muscle
5	chr4:79608400-79612200	Enhancers	K562	blood
6	chr4:79609000-79610800	Enhancers	NHEK	skin
7	chr4:79609000-79616000	Enhancers	NHDF-Ad	bronchial
8	chr4:79609200-79610800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:79609200-79611000	Enhancers	HMEC	breast
10	chr4:79609200-79612200	Enhancers	Fetal Heart	heart
11	chr4:79609200-79613200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr4:79609400-79610400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:79609600-79610200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:79609600-79610200	Enhancers	NHLF	lung
15	chr4:79609600-79610400	Enhancers	HSMM	muscle
16	chr4:79609600-79611400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:79609600-79612000	Enhancers	Placenta	Placenta
18	chr4:79609600-79612400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:79609600-79613600	Enhancers	Osteobl	bone
20	chr4:79609800-79610400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:79609800-79610400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:79610000-79616400	Enhancers	Fetal Intestine Large	intestine

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