Variant report

Variant	rs16834871
Chromosome Location	chr1:152996161-152996162
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152975139..152976833-chr1:152995006..152997182,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163209	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10157591	1.00[CEU][hapmap]
rs10494288	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10888521	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11205126	1.00[EUR][1000 genomes]
rs11205130	1.00[EUR][1000 genomes]
rs11205131	1.00[CEU][hapmap]
rs11205147	1.00[EUR][1000 genomes]
rs11205183	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11806470	1.00[EUR][1000 genomes]
rs12021601	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12022870	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12023643	1.00[EUR][1000 genomes]
rs12024694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12026519	1.00[CEU][hapmap]
rs12029192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12032522	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12036590	1.00[CEU][hapmap]
rs12036697	1.00[EUR][1000 genomes]
rs12037255	1.00[CEU][hapmap]
rs12037754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12046394	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs12047099	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12047187	0.94[ASN][1000 genomes]
rs12047225	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12047630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12047888	1.00[EUR][1000 genomes]
rs12239808	1.00[CEU][hapmap]
rs12239812	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12239814	1.00[CEU][hapmap]
rs1415973	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs167452	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs16834734	1.00[CEU][hapmap]
rs16834746	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16834751	1.00[CEU][hapmap]
rs16834838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1846857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1890284	0.83[CHB][hapmap]
rs1974141	1.00[EUR][1000 genomes]
rs1995307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2339383	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2339501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28647391	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2879485	1.00[CEU][hapmap]
rs310096	0.88[ASN][1000 genomes]
rs310097	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs310098	0.91[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs310099	0.88[ASN][1000 genomes]
rs310101	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs310104	0.91[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs310113	0.80[ASN][1000 genomes]
rs310116	0.80[ASN][1000 genomes]
rs310117	0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs310125	0.96[ASN][1000 genomes]
rs36090881	1.00[EUR][1000 genomes]
rs367220	0.87[ASN][1000 genomes]
rs373451	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3737862	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs374170	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs377182	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs3856020	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs399274	0.86[ASN][1000 genomes]
rs4041337	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4041340	1.00[EUR][1000 genomes]
rs418550	0.87[CHB][hapmap]
rs423692	0.91[CHB][hapmap]
rs4240863	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4240864	1.00[EUR][1000 genomes]
rs442209	0.87[ASN][1000 genomes]
rs454186	0.87[CHB][hapmap]
rs4845325	1.00[CEU][hapmap]
rs4845328	1.00[EUR][1000 genomes]
rs4845498	1.00[EUR][1000 genomes]
rs576793	0.88[ASN][1000 genomes]
rs58290373	1.00[EUR][1000 genomes]
rs593671	0.88[ASN][1000 genomes]
rs59837747	1.00[EUR][1000 genomes]
rs60500053	1.00[EUR][1000 genomes]
rs61491150	1.00[EUR][1000 genomes]
rs634639	0.94[ASN][1000 genomes]
rs649269	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6668295	1.00[EUR][1000 genomes]
rs72480203	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7525198	0.88[ASN][1000 genomes]
rs7532449	1.00[CEU][hapmap]
rs7552416	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
8	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
9	nsv1003756	chr1:152944201-153044621	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv3416199	chr1:152957887-153005113	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16834871	S100A13	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152994200-153000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:152995000-152997400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:152995600-152996800	Enhancers	Esophagus	oesophagus

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