Variant report

Variant	rs4519770
Chromosome Location	chr4:73877415-73877416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:73876629..73878196-chr4:73883041..73885471,2	K562	blood:
2	chr4:73872915..73876082-chr4:73876162..73879588,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10034689	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap]
rs10035001	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]
rs10050235	0.84[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap]
rs10805059	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap]
rs10938064	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10938065	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10938066	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11935070	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs13101277	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs13135890	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13141048	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13149759	0.80[JPT][hapmap]
rs1381014	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1460989	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1534450	0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4694155	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.83[ASN][1000 genomes]
rs4694156	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4995246	0.83[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs5020219	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]
rs6830954	0.83[ASN][1000 genomes]
rs6850870	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7664144	0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949371	chr4:73678470-74094500	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1005704	chr4:73708248-73907315	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv829971	chr4:73709753-73880451	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv432611	chr4:73740665-74099265	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv523169	chr4:73752242-74120910	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv998707	chr4:73753922-74044843	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv537136	chr4:73753922-74044843	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv917017	chr4:73754127-74044830	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1013174	chr4:73785324-74031884	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv537137	chr4:73785324-74031884	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv1012068	chr4:73817769-74003079	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv1014088	chr4:73817769-74031884	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv537138	chr4:73817769-74031884	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv533502	chr4:73819067-74044813	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4519770	AFP	cis	parietal	SCAN
rs4519770	NAAA	cis	cerebellum	SCAN
rs4519770	AFM	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:73876600-73878200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:73877200-73878800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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