Variant report

Variant	rs2817840
Chromosome Location	chr1:71475710-71475711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:71473756..71476164-chr1:71480981..71482752,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTH-14	chr1:71475401-71475924	l_71_chr1:71319635-71475982_testes

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10889905	0.92[ASN][1000 genomes]
rs11209730	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11209738	0.92[ASN][1000 genomes]
rs11800326	0.95[ASN][1000 genomes]
rs12060001	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1569593	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1883459	0.81[ASN][1000 genomes]
rs2268057	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2300164	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2300172	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300179	0.91[ASN][1000 genomes]
rs2744914	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34342579	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35631379	0.95[ASN][1000 genomes]
rs36075725	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3819783	0.84[EUR][1000 genomes]
rs3819790	0.84[EUR][1000 genomes]
rs5693	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66944390	0.96[ASN][1000 genomes]
rs9424957	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9424958	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9425052	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425053	0.95[ASN][1000 genomes]
rs9425054	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1845198	chr1:71274759-71514969	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv830148	chr1:71310366-71483932	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv871313	chr1:71391646-71489438	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1008902	chr1:71417926-71488139	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv534989	chr1:71417926-71488139	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv546472	chr1:71432984-71541003	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	555 gene(s)	inside rSNPs	diseases
7	nsv461851	chr1:71442626-71507541	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
8	nsv546473	chr1:71442626-71507541	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
9	esv1850593	chr1:71444149-71514969	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv870843	chr1:71465292-71489438	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv870734	chr1:71469583-71485036	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
12	nsv870576	chr1:71469583-71489438	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71465800-71485000	Weak transcription	Pancreas	Pancrea
2	chr1:71470600-71477600	Weak transcription	Adipose Nuclei	Adipose
3	chr1:71473600-71478000	Weak transcription	Aorta	Aorta
4	chr1:71474600-71478200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:71475200-71476200	Strong transcription	K562	blood
6	chr1:71475400-71478200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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