Variant report

Variant	rs1539492
Chromosome Location	chr1:151570241-151570242
allele	A/G
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151556628..151559025-chr1:151567592..151570969,4	MCF-7	breast:
2	1:151516085-151535167..1:151565791-151575769	H1-hESC	embryonic stem cell:	embryo
3	1:151427826-151434310..1:151565791-151575769	K562	blood:
4	1:151333184-151350267..1:151565791-151575769	GM12878	blood:
5	1:151565791-151575769..1:151618750-151636526	K562	blood:
6	1:151254384-151268403..1:151565791-151575769	K562	blood:
7	chr1:151511392..151513624-chr1:151569200..151573110,3	MCF-7	breast:
8	chr1:151568597..151570310-chr1:151583939..151586200,2	MCF-7	breast:
9	chr1:151511423..151515808-chr1:151564689..151570634,14	MCF-7	breast:
10	1:151496437-151509688..1:151565791-151575769	K562	blood:
11	chr1:151559403..151561467-chr1:151568084..151570388,2	MCF-7	breast:
12	chr1:151569147..151571647-chr1:151575005..151576628,2	MCF-7	breast:
13	1:151411623-151426875..1:151565791-151575769	Hela-S3	cervix:
14	chr1:151569138..151571685-chr1:151583171..151587169,4	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000143373	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000250734	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143416	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10888422	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1196359	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1196361	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1196362	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12749	0.90[MEX][hapmap]
rs1781415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2337363	0.87[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4394658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970920	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6660238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6683478	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6701819	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6702889	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	esv3390899	chr1:151570067-151570591	Weak transcription Enhancers	Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151555400-151580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:151566600-151574200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:151566800-151572000	Weak transcription	Fetal Heart	heart
4	chr1:151569600-151574200	Weak transcription	HepG2	liver
5	chr1:151569800-151570400	Enhancers	Hela-S3	cervix
6	chr1:151569800-151570800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:151570200-151574200	Weak transcription	K562	blood
8	chr1:151570200-151578600	Weak transcription	A549	lung

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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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