Variant report

Variant	rs253409
Chromosome Location	chr5:74928069-74928070
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10043621	0.87[ASN][1000 genomes]
rs10044053	0.90[ASN][1000 genomes]
rs10060260	0.85[ASN][1000 genomes]
rs10067641	0.96[ASN][1000 genomes]
rs1051795	0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs10942739	0.82[ASN][1000 genomes]
rs13354407	0.91[ASN][1000 genomes]
rs1427924	0.96[ASN][1000 genomes]
rs17739580	0.80[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1863934	0.94[ASN][1000 genomes]
rs1863935	0.94[ASN][1000 genomes]
rs1995267	0.91[ASN][1000 genomes]
rs2287711	0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs253392	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs253393	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs253408	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs253413	0.82[ASN][1000 genomes]
rs2878519	0.95[ASN][1000 genomes]
rs2878520	0.95[ASN][1000 genomes]
rs3213801	0.90[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs34340	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34344	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34345	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34350	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4045166	0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs4440336	0.81[ASN][1000 genomes]
rs4703674	0.91[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs4704228	0.81[ASN][1000 genomes]
rs57312935	0.87[ASN][1000 genomes]
rs5744533	0.95[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs5744555	0.90[CHB][hapmap]
rs5744575	0.89[ASN][1000 genomes]
rs5744595	0.86[ASN][1000 genomes]
rs5744598	0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs5744601	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs5744621	0.91[ASN][1000 genomes]
rs5744663	0.90[ASN][1000 genomes]
rs5744703	0.91[ASN][1000 genomes]
rs59506842	0.83[ASN][1000 genomes]
rs61430233	0.82[ASN][1000 genomes]
rs67969809	0.95[ASN][1000 genomes]
rs6861279	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6886841	0.95[ASN][1000 genomes]
rs7445415	0.89[ASN][1000 genomes]
rs767676	0.91[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs7706857	0.96[ASN][1000 genomes]
rs7709282	0.95[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7717505	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7723531	0.96[ASN][1000 genomes]
rs924452	0.96[ASN][1000 genomes]
rs9293656	0.85[ASN][1000 genomes]
rs9332464	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74913800-74933600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:74914000-74930800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:74916600-74931800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:74918400-74944200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:74918800-74934000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:74920200-74936600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:74920400-74929000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:74920400-74944200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:74920600-74933400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:74921800-74964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:74922000-74931600	Weak transcription	Lung	lung
12	chr5:74922000-74932000	Weak transcription	Aorta	Aorta
13	chr5:74922000-74932400	Weak transcription	Fetal Intestine Small	intestine
14	chr5:74926800-74929600	Enhancers	Fetal Heart	heart
15	chr5:74927400-74928400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:74928000-74928600	Enhancers	K562	blood

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