Variant report

Variant	rs16834728
Chromosome Location	chr1:152853137-152853138
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	chr1:152841334..152844015-chr1:152851385..152853978,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11205128	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[MEX][hapmap]
rs11205129	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs11205131	0.82[JPT][hapmap]
rs11801996	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs12021601	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs12022319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12022349	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs12022870	0.90[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs12047888	0.80[ASN][1000 genomes]
rs12048655	0.91[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs12568299	0.80[MEX][hapmap]
rs16834734	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2339383	0.91[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs3737861	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3737862	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4363387	0.91[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4845489	0.80[ASN][1000 genomes]
rs4845490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845492	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845494	0.91[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs60566199	0.81[ASN][1000 genomes]
rs6659798	0.82[CHD][hapmap];0.87[MEX][hapmap]
rs73006590	0.81[ASN][1000 genomes]
rs7553755	0.91[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7556490	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv999918	chr1:152749733-152861866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1000159	chr1:152809514-152853766	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1008447	chr1:152811171-152853748	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv2761937	chr1:152811183-152853760	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16834728	LCE6A	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152850800-152853800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:152850800-152853800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:152850800-152853800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:152851000-152853800	Enhancers	HMEC	breast
5	chr1:152852000-152853600	Enhancers	Liver	Liver
6	chr1:152852200-152853200	Enhancers	Esophagus	oesophagus
7	chr1:152852400-152853400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:152852600-152853600	Flanking Active TSS	NHEK	skin
9	chr1:152852800-152853600	Flanking Active TSS	GM12878-XiMat	blood

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