Variant report

Variant	rs2002153
Chromosome Location	chr4:57745811-57745812
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57741268..57742885-chr4:57744853..57746606,2	K562	blood:
2	chr4:57301034..57302862-chr4:57745174..57747943,2	K562	blood:

Variant related genes	Relation type
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10008356	0.87[ASN][1000 genomes]
rs10030913	0.92[ASN][1000 genomes]
rs10866440	0.92[ASN][1000 genomes]
rs10866441	0.81[ASN][1000 genomes]
rs1105434	0.84[ASN][1000 genomes]
rs11727329	0.85[EUR][1000 genomes]
rs11730321	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11730476	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11730525	0.94[ASN][1000 genomes]
rs11734953	0.90[ASN][1000 genomes]
rs11736192	0.82[ASN][1000 genomes]
rs11736869	0.84[ASN][1000 genomes]
rs11736965	0.83[ASN][1000 genomes]
rs11933908	0.94[ASN][1000 genomes]
rs12500454	0.84[ASN][1000 genomes]
rs12501224	0.81[ASN][1000 genomes]
rs12501990	0.84[ASN][1000 genomes]
rs12502076	0.80[ASN][1000 genomes]
rs13108245	0.90[ASN][1000 genomes]
rs13113802	0.91[ASN][1000 genomes]
rs13116564	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13125082	0.80[EUR][1000 genomes]
rs13130600	0.85[EUR][1000 genomes]
rs13136432	0.81[ASN][1000 genomes]
rs13146960	0.90[ASN][1000 genomes]
rs13149162	0.93[ASN][1000 genomes]
rs13150593	0.81[ASN][1000 genomes]
rs13152476	0.81[ASN][1000 genomes]
rs13353552	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1877669	0.94[ASN][1000 genomes]
rs2090962	0.96[ASN][1000 genomes]
rs2412761	0.87[AFR][1000 genomes]
rs3000	0.94[ASN][1000 genomes]
rs34124552	0.81[ASN][1000 genomes]
rs34448457	0.81[ASN][1000 genomes]
rs35267092	0.81[ASN][1000 genomes]
rs3806745	0.84[ASN][1000 genomes]
rs4276341	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4443350	0.90[AFR][1000 genomes]
rs4864606	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4864607	0.93[ASN][1000 genomes]
rs4864608	0.84[ASN][1000 genomes]
rs4865156	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4865157	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4865158	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4865159	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4865160	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55822707	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56122758	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56143151	0.89[AFR][1000 genomes]
rs62308110	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62308111	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62308135	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62308136	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62308137	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6554393	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6554394	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6554397	0.94[ASN][1000 genomes]
rs6554398	0.92[ASN][1000 genomes]
rs6816950	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6835102	0.91[ASN][1000 genomes]
rs6835108	0.91[ASN][1000 genomes]
rs6838948	0.94[ASN][1000 genomes]
rs6839845	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6840805	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6852110	0.84[ASN][1000 genomes]
rs6854420	0.94[ASN][1000 genomes]
rs6855212	0.96[ASN][1000 genomes]
rs6857005	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6857226	0.91[ASN][1000 genomes]
rs6858216	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs71601656	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs729844	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73242609	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7666804	0.96[ASN][1000 genomes]
rs7667302	0.96[ASN][1000 genomes]
rs7680734	0.84[ASN][1000 genomes]
rs7695970	0.94[ASN][1000 genomes]
rs899632	0.96[ASN][1000 genomes]
rs9684742	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv822561	chr4:57736121-57747867	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2002153	RP11-738E22.3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57738200-57746400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:57741400-57750800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr4:57744400-57748800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:57745000-57747000	Enhancers	GM12878-XiMat	blood
5	chr4:57745200-57746800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr4:57745200-57747200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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