Variant report

Variant	rs6854420
Chromosome Location	chr4:57770173-57770174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57766086..57769107-chr4:57769697..57772712,3	K562	blood:
2	chr4:57767984..57770283-chr4:57774532..57776047,2	MCF-7	breast:
3	chr4:57766348..57770252-chr4:57770939..57776427,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000084093	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10008356	0.93[ASN][1000 genomes]
rs10030913	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10866440	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10866441	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1105434	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11730321	0.90[ASN][1000 genomes]
rs11730476	0.90[ASN][1000 genomes]
rs11730525	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734953	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11736192	0.88[ASN][1000 genomes]
rs11736869	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11736965	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11737689	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11933908	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941568	0.91[EUR][1000 genomes]
rs12500454	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12501224	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12501990	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12502076	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13108245	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113802	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13116564	0.97[ASN][1000 genomes]
rs13119525	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13131605	0.85[ASN][1000 genomes]
rs13136432	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13146960	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13149162	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13150593	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13152476	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13353552	0.96[ASN][1000 genomes]
rs1877669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1963666	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2002153	0.94[ASN][1000 genomes]
rs2014870	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2090962	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2228991	0.81[ASN][1000 genomes]
rs3000	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34124552	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34448457	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35267092	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3796528	0.81[ASN][1000 genomes]
rs3806745	0.90[ASN][1000 genomes]
rs4276341	0.97[ASN][1000 genomes]
rs4864606	1.00[ASN][1000 genomes]
rs4864607	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864608	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865156	0.90[ASN][1000 genomes]
rs4865157	0.93[ASN][1000 genomes]
rs4865158	0.92[ASN][1000 genomes]
rs4865159	0.94[ASN][1000 genomes]
rs4865160	0.94[ASN][1000 genomes]
rs55822707	0.98[ASN][1000 genomes]
rs56122758	0.91[ASN][1000 genomes]
rs62308110	0.90[ASN][1000 genomes]
rs62308111	0.90[ASN][1000 genomes]
rs62308135	1.00[ASN][1000 genomes]
rs62308136	1.00[ASN][1000 genomes]
rs62308137	0.99[ASN][1000 genomes]
rs62308155	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554393	0.93[ASN][1000 genomes]
rs6554394	0.93[ASN][1000 genomes]
rs6554397	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554398	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554399	0.81[ASN][1000 genomes]
rs6816950	0.90[ASN][1000 genomes]
rs6835102	0.88[ASN][1000 genomes]
rs6835108	0.88[ASN][1000 genomes]
rs6838948	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839845	0.88[ASN][1000 genomes]
rs6840805	0.90[ASN][1000 genomes]
rs6852110	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6855212	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6857005	0.88[ASN][1000 genomes]
rs6857226	0.88[ASN][1000 genomes]
rs6858216	0.90[ASN][1000 genomes]
rs71601656	0.84[ASN][1000 genomes]
rs729844	0.97[ASN][1000 genomes]
rs73242609	1.00[ASN][1000 genomes]
rs7666804	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7667302	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7667744	0.91[EUR][1000 genomes]
rs7680734	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7695970	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899630	0.91[EUR][1000 genomes]
rs899631	0.91[EUR][1000 genomes]
rs899632	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9684742	0.97[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	nsv822562	chr4:57768655-57779715	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 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	chr4:57761600-57773000	Weak transcription	Right Atrium	heart
2	chr4:57768600-57770200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr4:57768800-57771000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr4:57769000-57770200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:57769000-57770200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:57769000-57770200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:57770000-57770200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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