Variant report

Variant	rs1923499
Chromosome Location	chr1:152413175-152413176
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:152160983..152163280-chr1:152412961..152414390,15	MCF-7	breast:
2	chr1:152160785..152161519-chr1:152413069..152413968,2	K562	blood:
3	chr1:152411861..152413555-chr1:152429926..152432618,2	MCF-7	breast:
4	chr1:152370937..152372499-chr1:152412540..152414323,43	MCF-7	breast:
5	chr1:152161080..152162827-chr1:152413067..152413987,7	MCF-7	breast:
6	chr1:152369672..152370659-chr1:152413047..152413901,4	MCF-7	breast:
7	chr1:152412473..152414075-chr1:152416605..152419173,2	K562	blood:
8	chr1:152370764..152372337-chr1:152412999..152414162,14	MCF-7	breast:
9	chr1:152379306..152381264-chr1:152411990..152414045,3	MCF-7	breast:
10	chr1:152370558..152373181-chr1:152412666..152414314,2	MCF-7	breast:
11	chr1:152162395..152164443-chr1:152410728..152413718,2	MCF-7	breast:
12	chr1:152162203..152163021-chr1:152413054..152413609,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000183586	Chromatin interaction
ENSG00000237975	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10888488	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205002	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11205003	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11205004	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11205008	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11578573	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11579024	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11579085	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11803629	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12069640	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12125681	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12749879	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16834090	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1885527	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1885528	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1885529	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1923491	0.92[CEU][hapmap]
rs1923498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4557976	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4636462	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845433	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845435	0.95[ASN][1000 genomes]
rs4845436	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845438	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845440	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845766	0.92[CEU][hapmap]
rs4845767	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845768	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845769	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845770	0.95[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845771	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845775	0.82[ASN][1000 genomes]
rs4991216	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs499997	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs556124	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587674	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6695950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529997	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7548609	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs986903	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv872443	chr1:152400055-152459747	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv872444	chr1:152400361-152440753	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv824664	chr1:152409024-152434443	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv463850	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv547858	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv872445	chr1:152411813-152440753	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152409400-152414800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:152409600-152414600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:152409800-152416600	Weak transcription	HSMM	muscle
4	chr1:152410200-152415400	Weak transcription	HSMMtube	muscle
5	chr1:152410600-152413600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:152410800-152413200	Weak transcription	NHEK	skin
7	chr1:152411600-152413200	Weak transcription	Esophagus	oesophagus
8	chr1:152413000-152413200	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr1:152413000-152413800	Enhancers	HMEC	breast
10	chr1:152413000-152416400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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