Variant report

Variant	rs6842686
Chromosome Location	chr4:79541206-79541207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79540489..79542069-chr4:79565977..79567685,2	K562	blood:
2	chr4:79539944..79542202-chr4:79696313..79698860,2	MCF-7	breast:
3	chr4:79539469..79541784-chr4:79542967..79545654,2	K562	blood:

Variant related genes	Relation type
ENSG00000251442	Chromatin interaction
ENSG00000138756	Chromatin interaction
ENSG00000260278	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10008069	0.92[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs10028815	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10029214	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10857035	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11098274	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098275	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098278	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11725235	0.81[JPT][hapmap]
rs11932080	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12510383	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12510411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12639656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12644222	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12711028	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13110339	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1346145	0.84[TSI][hapmap]
rs1532427	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1806906	0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap]
rs1834519	0.87[TSI][hapmap]
rs28579596	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34636970	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4254805	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4365753	0.87[TSI][hapmap]
rs4472163	0.84[TSI][hapmap]
rs4495064	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4560439	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs4612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4645238	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5942	0.81[JPT][hapmap]
rs5944	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62308286	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6533827	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6533828	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6817175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821449	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6822675	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6825328	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6842723	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6855458	0.87[TSI][hapmap]
rs7656801	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7659978	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7661370	0.81[JPT][hapmap]
rs7672835	0.87[CEU][hapmap]
rs7672903	0.85[JPT][hapmap]
rs7675464	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7675646	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7677783	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7694152	0.81[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6842686	ANXA3	cis	cerebellum	SCAN
rs6842686	CXCL10	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79491800-79542600	Weak transcription	NH-A	brain
2	chr4:79518000-79548000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:79518600-79543600	Weak transcription	Stomach Mucosa	stomach
4	chr4:79524200-79543400	Weak transcription	A549	lung
5	chr4:79527800-79542600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:79527800-79542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:79531400-79543000	Weak transcription	Hela-S3	cervix
8	chr4:79531800-79543200	Weak transcription	HUVEC	blood vessel
9	chr4:79533800-79548800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:79534600-79547800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:79535400-79542600	Weak transcription	Placenta	Placenta
12	chr4:79535600-79543000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:79536400-79550600	Weak transcription	Left Ventricle	heart
14	chr4:79536800-79542600	Weak transcription	Right Atrium	heart
15	chr4:79537000-79545800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:79537800-79542600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:79537800-79543400	Weak transcription	HSMM	muscle
18	chr4:79538200-79542800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:79538200-79543000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:79538400-79542400	Enhancers	K562	blood
21	chr4:79539200-79549800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:79539400-79550400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr4:79539600-79542600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:79539600-79542600	Weak transcription	NHDF-Ad	bronchial
25	chr4:79539600-79550000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:79539800-79545200	Weak transcription	GM12878-XiMat	blood
27	chr4:79540200-79543400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:79540800-79542600	Weak transcription	Fetal Intestine Large	intestine
29	chr4:79541000-79542200	Weak transcription	Fetal Intestine Small	intestine

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