Variant report

Variant	rs4896502
Chromosome Location	chr6:140292178-140292179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140287622..140289430-chr6:140290980..140292727,2	K562	blood:
2	chr6:140289417..140292711-chr6:140293441..140296166,4	K562	blood:
3	chr6:140283795..140286173-chr6:140291088..140293837,2	MCF-7	breast:
4	chr6:140291815..140294274-chr6:140303049..140305531,2	K562	blood:
5	chr6:140285910..140289430-chr6:140290980..140294749,5	K562	blood:
6	chr6:140281089..140284069-chr6:140290932..140294292,3	K562	blood:
7	chr6:139693951..139695871-chr6:140291667..140293357,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10499217	0.93[EUR][1000 genomes]
rs10499218	0.92[EUR][1000 genomes]
rs11751210	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs11753982	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11754152	0.99[EUR][1000 genomes]
rs11754864	0.99[EUR][1000 genomes]
rs11755397	0.96[EUR][1000 genomes]
rs11756192	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11758188	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11758612	0.99[EUR][1000 genomes]
rs11758718	0.90[EUR][1000 genomes]
rs11759030	0.99[EUR][1000 genomes]
rs1324127	0.90[EUR][1000 genomes]
rs1324129	0.90[EUR][1000 genomes]
rs13437223	1.00[ASN][1000 genomes]
rs13437498	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1361247	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1408295	1.00[GIH][hapmap];0.85[TSI][hapmap]
rs1582145	0.99[EUR][1000 genomes]
rs17069446	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17069692	0.99[EUR][1000 genomes]
rs17214668	0.88[EUR][1000 genomes]
rs17516817	1.00[JPT][hapmap]
rs17755520	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17755892	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17756503	0.93[EUR][1000 genomes]
rs17756562	0.92[EUR][1000 genomes]
rs17756688	0.92[EUR][1000 genomes]
rs17811661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17811691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17811871	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17812354	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17812384	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17812480	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17812617	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs17812647	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes]
rs17812736	0.96[EUR][1000 genomes]
rs1890428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1933741	0.97[EUR][1000 genomes]
rs201279	0.88[EUR][1000 genomes]
rs201280	0.89[EUR][1000 genomes]
rs2144168	1.00[JPT][hapmap]
rs35441484	0.99[EUR][1000 genomes]
rs477737	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs4895578	1.00[ASN][1000 genomes]
rs4895580	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4895581	0.92[EUR][1000 genomes]
rs4896504	0.92[EUR][1000 genomes]
rs4896505	0.85[EUR][1000 genomes]
rs4896506	0.85[EUR][1000 genomes]
rs496953	0.88[EUR][1000 genomes]
rs55732492	0.97[EUR][1000 genomes]
rs55738757	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55834276	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55902158	0.91[EUR][1000 genomes]
rs55907136	0.99[EUR][1000 genomes]
rs56022257	0.97[EUR][1000 genomes]
rs56030520	0.99[EUR][1000 genomes]
rs56202454	0.94[EUR][1000 genomes]
rs56296431	0.99[EUR][1000 genomes]
rs58650930	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs593265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59665575	0.97[EUR][1000 genomes]
rs597854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs638899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659714	0.90[EUR][1000 genomes]
rs661507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913694	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6925609	0.93[EUR][1000 genomes]
rs72975808	0.88[EUR][1000 genomes]
rs72975814	0.85[EUR][1000 genomes]
rs72988718	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72988720	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72988721	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72988724	0.92[EUR][1000 genomes]
rs72988734	0.99[EUR][1000 genomes]
rs72988736	0.92[EUR][1000 genomes]
rs72988741	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72988745	0.89[EUR][1000 genomes]
rs72988750	0.99[EUR][1000 genomes]
rs72988752	0.97[EUR][1000 genomes]
rs72988753	0.99[EUR][1000 genomes]
rs72988755	0.99[EUR][1000 genomes]
rs72988756	0.99[EUR][1000 genomes]
rs72988758	0.99[EUR][1000 genomes]
rs72988759	0.99[EUR][1000 genomes]
rs72988761	0.99[EUR][1000 genomes]
rs72990622	0.93[EUR][1000 genomes]
rs72990629	0.93[EUR][1000 genomes]
rs7769264	0.90[EUR][1000 genomes]
rs9484333	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9495604	1.00[YRI][hapmap]
rs9495609	1.00[ASN][1000 genomes]
rs9495610	1.00[ASN][1000 genomes]
rs9495619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9495621	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs953112	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4896502	PBOV1	cis	cerebellum	SCAN
rs4896502	TBC1D30	trans	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140284400-140292200	Weak transcription	Placenta	Placenta
2	chr6:140287000-140292600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:140287800-140299000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:140289200-140292400	Weak transcription	HSMM	muscle
5	chr6:140289200-140294400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:140289400-140294800	Weak transcription	HUVEC	blood vessel
7	chr6:140289600-140297200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:140291000-140294800	Weak transcription	K562	blood
9	chr6:140291400-140292200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:140291400-140292400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr6:140291400-140292400	Enhancers	NHEK	skin
12	chr6:140291600-140292200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:140291600-140292400	Enhancers	Osteobl	bone
14	chr6:140291600-140292600	Enhancers	NHDF-Ad	bronchial
15	chr6:140291600-140302000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:140291800-140292200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:140291800-140292200	Enhancers	HMEC	breast
18	chr6:140292000-140292200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:140292000-140292200	Enhancers	NH-A	brain
20	chr6:140292000-140292400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:140292000-140292800	Enhancers	Primary B cells from peripheral blood	blood

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