Variant report

Variant	rs1019677
Chromosome Location	chr3:101263573-101263574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:40001641..40002163-chr3:101263430..101263949,2	MCF-7	breast:
2	chr3:101262295..101266034-chr3:101290891..101293840,3	MCF-7	breast:
3	chr3:101214465..101215044-chr3:101263439..101263951,2	MCF-7	breast:
4	chr3:101231701..101233998-chr3:101261738..101264309,2	MCF-7	breast:
5	chr2:40000146..40001663-chr3:101262826..101264500,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138468	Chromatin interaction
ENSG00000081154	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10936607	0.90[EUR][1000 genomes]
rs10936642	0.84[EUR][1000 genomes]
rs10936664	0.94[EUR][1000 genomes]
rs12491955	0.84[EUR][1000 genomes]
rs12496260	0.93[EUR][1000 genomes]
rs13062095	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13087404	0.90[EUR][1000 genomes]
rs13088318	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13320918	0.91[EUR][1000 genomes]
rs13322987	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16843927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1918405	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141179	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2141180	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.92[EUR][1000 genomes]
rs2162304	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2178036	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2250611	0.90[EUR][1000 genomes]
rs2317699	0.90[EUR][1000 genomes]
rs2317700	0.89[EUR][1000 genomes]
rs2317745	0.89[EUR][1000 genomes]
rs2317749	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs2317751	0.88[EUR][1000 genomes]
rs2433031	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2553416	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes]
rs2553424	0.88[EUR][1000 genomes]
rs2553427	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes]
rs2553430	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes]
rs2682383	0.89[EUR][1000 genomes]
rs2682384	0.89[EUR][1000 genomes]
rs2682386	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs2682390	0.89[EUR][1000 genomes]
rs2682391	0.90[EUR][1000 genomes]
rs28460520	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28565548	0.87[EUR][1000 genomes]
rs34255148	0.92[EUR][1000 genomes]
rs3846091	0.94[EUR][1000 genomes]
rs4287896	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580527	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4683899	0.90[EUR][1000 genomes]
rs4683900	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes]
rs4683917	0.91[EUR][1000 genomes]
rs4683918	0.91[EUR][1000 genomes]
rs473702	0.87[EUR][1000 genomes]
rs497953	0.87[EUR][1000 genomes]
rs520558	0.87[EUR][1000 genomes]
rs551442	0.87[EUR][1000 genomes]
rs56075912	0.90[EUR][1000 genomes]
rs6441602	0.88[EUR][1000 genomes]
rs6441608	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.92[EUR][1000 genomes]
rs6441610	0.94[EUR][1000 genomes]
rs6771561	0.93[EUR][1000 genomes]
rs6772703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6773536	0.90[EUR][1000 genomes]
rs7628681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631506	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636475	0.89[EUR][1000 genomes]
rs9814991	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9843186	0.91[EUR][1000 genomes]
rs9856435	0.94[EUR][1000 genomes]
rs9859077	0.91[CEU][hapmap];0.90[CHD][hapmap];0.82[TSI][hapmap]
rs9874188	0.83[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1019677	ZNF671	trans	multi-tissue	Pritchard
rs1019677	ZNF274	trans	multi-tissue	Pritchard
rs1019677	ZNF256	trans	multi-tissue	Pritchard
rs1019677	SENP7	Cis_1M	lymphoblastoid	RTeQTL
rs1019677	ZNF447	trans	multi-tissue	Pritchard
rs1019677	ZNF329	trans	multi-tissue	Pritchard

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101260600-101263600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr3:101260600-101263600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr3:101260600-101263800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:101260600-101263800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:101260600-101263800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:101260800-101263600	Enhancers	Primary T cells from cord blood	blood
7	chr3:101260800-101263600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:101260800-101263800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:101260800-101263800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:101261000-101266600	Weak transcription	HepG2	liver
11	chr3:101261200-101263600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr3:101261600-101267400	Weak transcription	K562	blood
13	chr3:101262000-101263800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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