Variant report

Variant	rs28540041
Chromosome Location	chr4:93355775-93355776
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10000919	0.81[ASN][1000 genomes]
rs10011953	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097337	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11930169	0.83[ASN][1000 genomes]
rs11942220	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11942235	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11942274	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11945497	0.83[ASN][1000 genomes]
rs12643954	0.83[ASN][1000 genomes]
rs12650010	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13109229	0.86[ASN][1000 genomes]
rs13141149	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35049432	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35182550	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36039865	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57390091	0.83[ASN][1000 genomes]
rs62311046	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62312219	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6532370	0.83[ASN][1000 genomes]
rs6826363	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6831486	0.85[ASN][1000 genomes]
rs6848180	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6849247	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7658053	0.81[ASN][1000 genomes]
rs7668752	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7674480	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7676323	0.83[ASN][1000 genomes]
rs7677007	0.82[ASN][1000 genomes]
rs7678325	0.83[ASN][1000 genomes]
rs7681461	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7681849	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9993173	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530154	chr4:92396539-93359983	Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1009960	chr4:92747531-93389054	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv461587	chr4:92837584-93376231	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv594866	chr4:92837584-93376231	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv948712	chr4:93007985-93740409	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv594868	chr4:93190198-93391251	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1000700	chr4:93270083-93425831	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv537182	chr4:93270083-93425831	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv997925	chr4:93270083-93464386	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv537183	chr4:93270083-93464386	Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:93344000-93364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:93353600-93355800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr4:93353600-93356200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr4:93354200-93356200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr4:93354600-93356200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr4:93354600-93356400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:93354600-93356600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:93354600-93356600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr4:93354600-93358400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:93354800-93358400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:93354800-93358400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:93354800-93359800	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr4:93354800-93361600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:93355600-93356200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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