Variant report

Variant	rs603671
Chromosome Location	chr10:43157138-43157139
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	chr10:43148790..43150722-chr10:43156364..43159356,2	K562	blood:
2	chr10:43141512..43143238-chr10:43157022..43158551,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BMS1-5	chr10:43156176-43157224	NONHSAT012919

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11239762	1.00[CHB][hapmap]
rs12246683	1.00[CHB][hapmap]
rs12254233	1.00[CHB][hapmap]
rs12262877	1.00[CHB][hapmap]
rs12264895	0.95[EUR][1000 genomes]
rs13376880	1.00[CHB][hapmap]
rs1539295	1.00[CHB][hapmap]
rs17158044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1831915	0.89[ASN][1000 genomes]
rs1855444	1.00[JPT][hapmap]
rs1855460	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs1889310	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs209375	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209376	0.83[EUR][1000 genomes]
rs209377	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209380	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs209381	0.83[EUR][1000 genomes]
rs209385	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap]
rs209386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209387	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209388	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209389	0.91[EUR][1000 genomes]
rs209390	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209391	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs209392	0.89[EUR][1000 genomes]
rs210221	0.89[ASN][1000 genomes]
rs210222	0.89[ASN][1000 genomes]
rs210236	0.89[ASN][1000 genomes]
rs210240	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs210259	0.81[ASN][1000 genomes]
rs210260	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs210263	0.89[ASN][1000 genomes]
rs210267	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs210280	1.00[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs210281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210285	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs210299	0.89[EUR][1000 genomes]
rs210300	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740329	1.00[CEU][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs4450129	1.00[CHB][hapmap]
rs522701	0.82[EUR][1000 genomes]
rs549167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55766110	0.89[ASN][1000 genomes]
rs574720	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs630838	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs644175	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs68055	0.89[ASN][1000 genomes]
rs683538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7072200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073731	0.95[EUR][1000 genomes]
rs7076849	0.88[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs7088389	0.95[EUR][1000 genomes]
rs7099013	0.95[EUR][1000 genomes]
rs7893674	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs7908362	1.00[CHB][hapmap]
rs7908372	1.00[CHB][hapmap]
rs7911186	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs7919712	0.88[CEU][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs9422635	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv895064	chr10:42783481-43243325	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv469725	chr10:42965130-43178323	Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv482513	chr10:42965130-43178323	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
11	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
12	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	esv34929	chr10:43116194-43329770	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs603671	HSD17B7P2	cis	parietal	SCAN
rs603671	ZNF33B	cis	parietal	SCAN
rs603671	CXCL12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43156400-43157200	Enhancers	K562	blood
2	chr10:43156400-43160400	Weak transcription	HepG2	liver

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