Variant report

Variant	rs12504135
Chromosome Location	chr4:55505933-55505934
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55500450..55502781-chr4:55503910..55506040,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10488849	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11722325	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11727273	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11940731	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12499367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106834	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2159935	0.85[JPT][hapmap]
rs2192158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2192159	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237029	0.86[JPT][hapmap]
rs2237030	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2237037	0.96[CEU][hapmap]
rs2237038	0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2537863	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35960771	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3819386	0.90[EUR][1000 genomes]
rs3819391	0.90[EUR][1000 genomes]
rs3819393	0.90[EUR][1000 genomes]
rs4864913	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554193	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554194	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554195	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6554197	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554198	0.82[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs6554199	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs6554200	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs6815651	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6825293	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs723585	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7656088	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7679314	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7695300	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs981959	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs999020	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs999021	0.81[JPT][hapmap];0.91[EUR][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	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv997430	chr4:55253397-55529288	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1004488	chr4:55440944-55511101	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1009708	chr4:55440944-55513275	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1010702	chr4:55440944-55528450	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1003671	chr4:55445652-55513275	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv521933	chr4:55449616-55512066	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12504135	SRD5A3	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55501800-55506600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr4:55501800-55506600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:55505200-55506000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:55505400-55506000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:55505400-55506200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr4:55505800-55506000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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