Variant report

Variant	rs1901519
Chromosome Location	chr5:101754473-101754474
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:101754300..101756641-chr5:101769503..101772313,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10041015	1.00[CHB][hapmap]
rs10041536	0.81[CHB][hapmap]
rs10041652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10044561	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10052669	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs10052881	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10054879	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs10055840	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs10057361	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10062073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10062241	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10063981	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10072122	0.84[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap]
rs10073892	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];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10074392	1.00[ASW][hapmap];0.85[TSI][hapmap]
rs10074590	0.81[CHB][hapmap]
rs10078945	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10479190	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs10479214	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10479218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479239	0.83[TSI][hapmap]
rs11745781	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13355136	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1376899	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1901513	1.00[CHB][hapmap]
rs1901514	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1901515	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs61522296	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62369688	0.85[ASN][1000 genomes]
rs6860730	1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs6881472	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6884301	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs6892179	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7356787	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap]
rs7729674	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs9327814	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9327821	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817537	chr5:101489151-101992104	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1016176	chr5:101534391-102333606	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv537831	chr5:101534391-102333606	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv522882	chr5:101596633-101782930	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1029894	chr5:101620079-102516827	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv830427	chr5:101651510-101849723	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv882511	chr5:101669015-101819981	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv882514	chr5:101672238-101795490	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv882515	chr5:101672238-101816104	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv882516	chr5:101672238-101819981	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv519686	chr5:101701924-101795490	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv526352	chr5:101701924-101795490	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1901519	SLCO4C1	cis	parietal	SCAN
rs1901519	PAM	cis	multi-tissue	Pritchard

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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