Variant report

Variant	rs6601210
Chromosome Location	chr5:177502019-177502020
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177487426..177490684-chr5:177499870..177503540,6	MCF-7	breast:
2	chr5:177501419..177502360-chr5:177590834..177591606,2	MCF-7	breast:
3	chr5:177501697..177504213-chr5:177591453..177593229,2	K562	blood:
4	chr5:177487397..177490398-chr5:177500448..177504603,3	MCF-7	breast:
5	chr5:177501753..177504683-chr5:177581029..177582623,2	K562	blood:
6	chr5:177500192..177502882-chr5:177557753..177559372,2	K562	blood:
7	chr5:177407733..177409330-chr5:177502018..177504540,2	MCF-7	breast:
8	chr5:177501622..177505245-chr5:177630293..177635895,8	MCF-7	breast:
9	chr5:177501649..177503512-chr5:177630511..177633228,3	K562	blood:
10	chr5:177501438..177504089-chr5:177638746..177641033,2	K562	blood:
11	chr5:177500972..177503850-chr5:177659363..177662027,2	K562	blood:
12	chr5:177501503..177502236-chr5:177590952..177591862,3	K562	blood:
13	chr5:177501352..177502104-chr5:177572551..177573321,2	MCF-7	breast:
14	chr5:177500353..177503253-chr5:177580681..177583610,3	K562	blood:
15	chr5:177500192..177502241-chr5:177557753..177559808,2	K562	blood:
16	chr5:177501683..177503355-chr5:177590379..177593305,3	K562	blood:

No data

No data

No data

Variant related genes	Relation type
ENSG00000145916	Chromatin interaction
ENSG00000145912	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000251211	Chromatin interaction
ENSG00000175309	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10052107	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10055575	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10064472	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10066407	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13165367	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074778	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs4246820	0.82[ASN][1000 genomes]
rs4246824	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4318801	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62390494	0.97[ASN][1000 genomes]
rs6865719	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030383	chr5:177310325-177571254	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv883186	chr5:177376317-177549491	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
4	nsv1021198	chr5:177386267-177611648	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1021060	chr5:177386344-177539867	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv600391	chr5:177488281-177549491	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6601210	ZNF354A	cis	parietal	SCAN
rs6601210	LOC202181	cis	cerebellum	SCAN
rs6601210	CPLX2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177493400-177506800	Weak transcription	Right Atrium	heart
2	chr5:177495800-177502600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:177497800-177502600	Weak transcription	Fetal Thymus	thymus
4	chr5:177501400-177502200	Bivalent Enhancer	HepG2	liver
5	chr5:177501600-177502200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:177501600-177503400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:177501600-177504000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:177501800-177502800	Enhancers	Hela-S3	cervix
9	chr5:177502000-177503000	Weak transcription	K562	blood

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Input of quick search could be:

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

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