Variant report

Variant	rs4131315
Chromosome Location	chr3:54459688-54459689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12632768	0.80[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap]
rs13082754	0.83[YRI][hapmap]
rs1449333	0.95[CEU][hapmap];0.87[JPT][hapmap]
rs1473348	0.88[GIH][hapmap]
rs1530732	0.83[CHD][hapmap]
rs1868502	0.80[EUR][1000 genomes]
rs1868508	0.83[JPT][hapmap]
rs1992963	0.95[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1992964	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2359789	0.96[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs2359790	0.85[GIH][hapmap];0.83[JPT][hapmap]
rs2359793	0.89[GIH][hapmap];0.83[JPT][hapmap]
rs4025912	0.89[GIH][hapmap];0.83[JPT][hapmap]
rs4974369	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4974370	0.80[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs6445660	0.87[ASN][1000 genomes]
rs6445664	0.82[CHD][hapmap]
rs6768189	0.81[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs6804196	0.93[GIH][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap]
rs73089420	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs731508	0.93[GIH][hapmap];0.89[TSI][hapmap]
rs7426795	0.83[CEU][hapmap]
rs7428295	0.81[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7429237	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7648293	0.80[JPT][hapmap]
rs7652529	0.90[ASN][1000 genomes]
rs7653648	0.82[GIH][hapmap]
rs9817603	0.93[GIH][hapmap];0.92[TSI][hapmap]
rs9827201	0.81[JPT][hapmap]
rs9836159	0.80[JPT][hapmap]
rs9843412	0.93[GIH][hapmap];0.92[TSI][hapmap]
rs9855860	0.80[JPT][hapmap]
rs9861155	0.87[JPT][hapmap]
rs9870407	0.93[GIH][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs9882285	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9882299	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9882553	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1010348	chr3:54435563-54508115	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv876807	chr3:54453655-54501086	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv998970	chr3:54455794-54516789	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv876808	chr3:54459688-54501086	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv876809	chr3:54459688-54501086	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4131315	TKT	cis	parietal	SCAN
rs4131315	HESX1	cis	cerebellum	SCAN
rs4131315	PCBP4	cis	parietal	SCAN
rs4131315	DNASE1L3	cis	parietal	SCAN
rs4131315	PRKCD	cis	cerebellum	SCAN
rs4131315	SEMA3G	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54458200-54463000	Enhancers	Hela-S3	cervix
2	chr3:54458600-54459800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:54458800-54461600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:54458800-54461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:54458800-54461800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:54458800-54461800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:54458800-54462600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:54459600-54459800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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