Variant report

Variant	rs2199039
Chromosome Location	chr4:69825188-69825189
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10019619	0.84[EUR][1000 genomes]
rs10027817	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10084885	0.80[AFR][1000 genomes]
rs11249517	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249518	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11723822	0.84[AFR][1000 genomes]
rs12505263	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512098	0.83[EUR][1000 genomes]
rs12512735	0.80[AFR][1000 genomes]
rs12719832	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12719833	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12719834	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12719835	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13128177	0.88[EUR][1000 genomes]
rs13144340	0.80[AFR][1000 genomes]
rs13145165	0.84[EUR][1000 genomes]
rs1379812	0.86[AFR][1000 genomes]
rs1458229	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1458230	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1598903	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1841055	0.84[EUR][1000 genomes]
rs1902923	0.88[EUR][1000 genomes]
rs1902935	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1902936	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2011000	0.83[EUR][1000 genomes]
rs2013866	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2168842	0.88[EUR][1000 genomes]
rs2199040	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331563	0.80[AFR][1000 genomes]
rs2331627	0.84[EUR][1000 genomes]
rs28485675	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3749510	0.86[EUR][1000 genomes]
rs3886642	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3886643	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4146121	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4487432	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4694490	0.82[EUR][1000 genomes]
rs4694491	0.82[EUR][1000 genomes]
rs60931562	0.83[EUR][1000 genomes]
rs6812186	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6812415	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6817568	0.90[EUR][1000 genomes]
rs6828317	0.83[EUR][1000 genomes]
rs6831147	0.86[EUR][1000 genomes]
rs6837000	0.87[EUR][1000 genomes]
rs6839405	0.88[EUR][1000 genomes]
rs6843788	0.83[EUR][1000 genomes]
rs6847948	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7673174	0.85[EUR][1000 genomes]
rs7679122	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7690181	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7691258	0.85[EUR][1000 genomes]
rs7691445	0.85[EUR][1000 genomes]
rs7695476	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs988887	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9998014	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005513	chr4:69446718-69890307	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	esv3398036	chr4:69700493-69841391	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv436447	chr4:69743339-69851390	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv967758	chr4:69780530-69870183	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv829962	chr4:69786869-69910283	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv10519	chr4:69816500-69835939	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69815200-69825600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:69820200-69825600	Weak transcription	Pancreas	Pancrea
3	chr4:69820200-69828400	Weak transcription	Liver	Liver
4	chr4:69820400-69825800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:69820400-69830000	Weak transcription	Small Intestine	intestine
6	chr4:69824600-69828200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:69824800-69825200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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