Variant report

Variant	rs4560439
Chromosome Location	chr4:79611844-79611845
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:79530292..79533218-chr4:79611643..79613326,2	K562	blood:
2	chr4:79515008..79517115-chr4:79611076..79613175,2	K562	blood:
3	chr4:79611783..79613882-chr4:79614566..79616143,2	MCF-7	breast:
4	chr4:79608933..79617994-chr4:79691426..79702696,23	K562	blood:
5	chr4:79602819..79606934-chr4:79608237..79614104,8	K562	blood:
6	chr4:79599061..79602262-chr4:79610175..79613299,3	K562	blood:
7	chr4:79610837..79614309-chr4:79701098..79703975,3	K562	blood:
8	chr4:79603993..79609685-chr4:79610850..79614972,9	K562	blood:
9	chr4:79581907..79584896-chr4:79611311..79615634,4	K562	blood:
10	chr4:79581907..79584896-chr4:79611311..79614789,3	K562	blood:
11	chr4:79549039..79550674-chr4:79611784..79614679,2	K562	blood:
12	chr4:79609796..79611994-chr4:79696295..79698982,2	MCF-7	breast:
13	chr4:79608764..79617994-chr4:79689698..79699789,21	K562	blood:
14	chr4:79592136..79594620-chr4:79610226..79611962,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260278	Chromatin interaction
ENSG00000138756	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10008008	0.95[EUR][1000 genomes]
rs10008069	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10028815	0.87[MEX][hapmap]
rs10029214	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs10084949	0.88[EUR][1000 genomes]
rs10857035	0.80[AMR][1000 genomes]
rs1134123	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1134124	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11724233	0.80[CHB][hapmap]
rs11931947	0.84[EUR][1000 genomes]
rs11932080	0.80[AMR][1000 genomes]
rs13101964	0.85[EUR][1000 genomes]
rs13110339	0.87[JPT][hapmap];0.80[AMR][1000 genomes]
rs13133277	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1346144	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1346145	0.95[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1469289	0.88[EUR][1000 genomes]
rs1469290	0.88[EUR][1000 genomes]
rs1532427	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs1582759	0.88[EUR][1000 genomes]
rs17434286	1.00[LWK][hapmap]
rs1806906	0.80[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1834519	0.95[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs1966537	0.87[EUR][1000 genomes]
rs28579596	0.80[AMR][1000 genomes]
rs2867465	0.97[EUR][1000 genomes]
rs2867466	0.97[EUR][1000 genomes]
rs2903578	0.88[EUR][1000 genomes]
rs4074675	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4254805	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4257676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321658	0.99[EUR][1000 genomes]
rs4365753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472162	0.86[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes]
rs4472163	0.87[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs4495064	0.80[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs4612	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4619914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533827	0.80[AMR][1000 genomes]
rs6533940	0.97[EUR][1000 genomes]
rs6533951	0.80[CHB][hapmap]
rs6815367	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6818230	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6825593	0.91[EUR][1000 genomes]
rs6842686	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs6842723	0.80[CHB][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs6855458	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]
rs7656801	0.80[AMR][1000 genomes]
rs7672208	0.90[EUR][1000 genomes]
rs7675464	0.80[AMR][1000 genomes]
rs7677162	0.90[EUR][1000 genomes]
rs7677783	0.80[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs7688534	1.00[LWK][hapmap]
rs7694971	0.90[EUR][1000 genomes]
rs7699519	0.90[EUR][1000 genomes]
rs7699905	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9992088	0.88[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4560439	LOC643424	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79605800-79612200	Weak transcription	Fetal Intestine Small	intestine
2	chr4:79606600-79612200	Weak transcription	HSMMtube	muscle
3	chr4:79608400-79612200	Enhancers	K562	blood
4	chr4:79609000-79616000	Enhancers	NHDF-Ad	bronchial
5	chr4:79609200-79612200	Enhancers	Fetal Heart	heart
6	chr4:79609200-79613200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr4:79609600-79612000	Enhancers	Placenta	Placenta
8	chr4:79609600-79612400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:79609600-79613600	Enhancers	Osteobl	bone
10	chr4:79610000-79616400	Enhancers	Fetal Intestine Large	intestine
11	chr4:79610200-79612400	Weak transcription	NHLF	lung
12	chr4:79610200-79612600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:79610400-79612200	Weak transcription	HSMM	muscle
14	chr4:79610400-79612400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:79610400-79612600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:79610400-79613200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:79610600-79617800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:79610800-79612000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:79610800-79612200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:79610800-79612800	Weak transcription	NHEK	skin
21	chr4:79611000-79613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:79611200-79612400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:79611400-79612600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:79611400-79616200	Enhancers	Primary hematopoietic stem cells	blood
25	chr4:79611600-79612600	Weak transcription	Hela-S3	cervix
26	chr4:79611600-79615200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr4:79611800-79616400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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