Variant report

Variant	rs4731453
Chromosome Location	chr7:128055016-128055017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:128048742..128050637-chr7:128053942..128056438,2	MCF-7	breast:
2	chr7:128053660..128055460-chr7:128057168..128058890,2	K562	blood:
3	chr7:128044666..128048176-chr7:128052474..128055557,4	MCF-7	breast:
4	chr7:128050564..128052309-chr7:128052445..128055482,3	K562	blood:

Variant related genes	Relation type
ENSG00000106348	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10229016	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10229394	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10230632	0.84[AMR][1000 genomes]
rs10230965	1.00[JPT][hapmap]
rs10245559	0.84[AMR][1000 genomes]
rs10251597	1.00[JPT][hapmap]
rs1035971	0.92[TSI][hapmap]
rs1065267	0.89[CEU][hapmap]
rs11770116	0.88[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11980741	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]
rs12672625	1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs13245629	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs1560214	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17537088	0.83[CEU][hapmap]
rs2288548	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402892	0.88[TSI][hapmap]
rs2402895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562730	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2562732	0.83[AMR][1000 genomes]
rs2562733	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2562734	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2562737	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs2562740	1.00[JPT][hapmap]
rs2732394	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2732397	0.88[AMR][1000 genomes]
rs2732429	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2732432	0.84[AMR][1000 genomes]
rs3097361	0.87[AMR][1000 genomes]
rs3793165	0.81[AFR][1000 genomes]
rs4728108	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4731446	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4731448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731450	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731454	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4731455	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6467178	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6947697	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6948333	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs930106	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv889191	chr7:127973133-128073326	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv365688	chr7:128052490-128056108	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4731453	FAM71F2	cis	cerebellum	SCAN
rs4731453	TMEM209	cis	parietal	SCAN
rs4731453	ZNF800	cis	parietal	SCAN
rs4731453	IL31RA	trans	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128050800-128062200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:128051200-128055400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:128051400-128086200	Weak transcription	Right Atrium	heart
4	chr7:128053800-128055200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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