Variant report

Variant	rs10004505
Chromosome Location	chr4:74437998-74437999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AFM-3	chr4:74437925-74438192	l_2664_chr4:74426244-74438192_liver

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10009048	0.84[AMR][1000 genomes]
rs10011419	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10011536	0.83[AMR][1000 genomes]
rs10016403	0.88[EUR][1000 genomes]
rs10019146	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10019320	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10020054	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10021827	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10029673	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10938077	0.82[EUR][1000 genomes]
rs10938078	0.82[EUR][1000 genomes]
rs10938079	0.82[EUR][1000 genomes]
rs10938088	0.83[AMR][1000 genomes]
rs11728915	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11729144	0.82[AMR][1000 genomes]
rs11943798	0.89[EUR][1000 genomes]
rs1247593	0.82[EUR][1000 genomes]
rs1247651	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1247659	0.84[AMR][1000 genomes]
rs1247668	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1247670	0.90[ASN][1000 genomes]
rs12503916	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12504448	0.82[EUR][1000 genomes]
rs12505842	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12506668	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12506675	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12507775	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13115877	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13135124	0.82[AMR][1000 genomes]
rs13144296	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13149172	0.83[AMR][1000 genomes]
rs13353732	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1528915	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1528916	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1528917	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1528918	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1569207	0.84[AMR][1000 genomes]
rs1590115	0.88[EUR][1000 genomes]
rs1590116	0.88[EUR][1000 genomes]
rs16849628	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849629	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849651	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849656	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849659	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849675	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849677	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849727	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17192413	0.90[ASN][1000 genomes]
rs1881611	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1919469	0.87[EUR][1000 genomes]
rs1919479	0.87[EUR][1000 genomes]
rs1997332	0.82[EUR][1000 genomes]
rs1997333	0.82[EUR][1000 genomes]
rs2008288	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2040354	0.81[EUR][1000 genomes]
rs2071097	0.82[EUR][1000 genomes]
rs2141465	0.82[EUR][1000 genomes]
rs2141470	0.86[EUR][1000 genomes]
rs2178290	0.82[EUR][1000 genomes]
rs28407399	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28450939	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28612539	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28693538	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28838047	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34123018	0.90[ASN][1000 genomes]
rs34773614	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34832471	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34859660	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756073	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4235119	0.82[EUR][1000 genomes]
rs4267703	0.82[EUR][1000 genomes]
rs4267704	0.82[EUR][1000 genomes]
rs4267705	0.82[EUR][1000 genomes]
rs4574378	0.88[EUR][1000 genomes]
rs4618279	0.88[EUR][1000 genomes]
rs62312137	0.82[AMR][1000 genomes]
rs6446937	0.82[EUR][1000 genomes]
rs6446938	0.82[EUR][1000 genomes]
rs6837506	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6852149	0.82[EUR][1000 genomes]
rs7665563	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7665972	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7667019	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7667185	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674913	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7676850	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7676870	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7676884	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7682201	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7687216	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7695792	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7695946	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7696502	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs997478	0.82[AMR][1000 genomes]
rs9997572	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9999939	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1792624	chr4:74437054-74453857	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74434400-74439600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:74437600-74438000	ZNF genes & repeats	Fetal Thymus	thymus
3	chr4:74437600-74440400	Enhancers	Dnd41	blood
4	chr4:74437800-74438000	ZNF genes & repeats	Thymus	Thymus
5	chr4:74437800-74438200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:74437800-74439400	Weak transcription	Fetal Intestine Small	intestine

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