Variant report

Variant	rs2373780
Chromosome Location	chr2:40248527-40248528
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	chr2:40248216..40251072-chr2:40272085..40274359,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1013954	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1023583	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779927	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10779928	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10865162	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11124723	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11124724	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11124726	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11124727	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11683512	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712678	0.91[ASN][1000 genomes]
rs12712679	0.97[ASN][1000 genomes]
rs13390026	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13430953	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1541565	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1541566	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1541567	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1548876	0.88[EUR][1000 genomes]
rs17024746	0.84[ASN][1000 genomes]
rs17024750	0.83[ASN][1000 genomes]
rs17024767	0.91[ASN][1000 genomes]
rs17024775	0.91[ASN][1000 genomes]
rs17024784	0.91[ASN][1000 genomes]
rs17024801	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024804	0.87[ASN][1000 genomes]
rs17024807	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17024825	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17024827	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17024830	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17024833	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17024837	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17024839	0.97[ASN][1000 genomes]
rs17024849	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17024875	0.97[ASN][1000 genomes]
rs2160210	0.95[ASN][1000 genomes]
rs2215974	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2373781	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2373784	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2373787	0.83[CHB][hapmap]
rs28491259	0.95[ASN][1000 genomes]
rs28649544	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34854449	0.94[ASN][1000 genomes]
rs4335994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4420745	0.99[ASN][1000 genomes]
rs4507140	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4519500	0.88[EUR][1000 genomes]
rs4538248	0.87[ASN][1000 genomes]
rs4580426	0.96[ASN][1000 genomes]
rs4952411	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56865237	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57416940	0.96[ASN][1000 genomes]
rs57465227	0.82[AMR][1000 genomes]
rs57677588	0.89[EUR][1000 genomes]
rs57707701	0.83[ASN][1000 genomes]
rs58224754	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59059664	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59073176	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59110768	0.85[ASN][1000 genomes]
rs59469973	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61023112	0.93[ASN][1000 genomes]
rs61604673	0.84[ASN][1000 genomes]
rs62148688	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62148691	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62148694	0.96[ASN][1000 genomes]
rs62148695	0.96[ASN][1000 genomes]
rs62148715	0.85[ASN][1000 genomes]
rs62150228	0.87[EUR][1000 genomes]
rs62151491	0.91[ASN][1000 genomes]
rs62151493	0.87[ASN][1000 genomes]
rs62151494	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62151495	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62151497	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6544280	0.89[EUR][1000 genomes]
rs6544282	0.89[EUR][1000 genomes]
rs6544296	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6731048	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6759636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760978	0.82[EUR][1000 genomes]
rs72940717	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7557819	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7558203	0.82[ASN][1000 genomes]
rs7564200	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7565837	0.85[ASN][1000 genomes]
rs7590992	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7591069	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7591263	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs759356	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs759357	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs759358	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7599493	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7607156	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7607499	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8179517	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs917970	0.89[EUR][1000 genomes]
rs9677667	0.81[AMR][1000 genomes]
rs9679646	0.84[AMR][1000 genomes]
rs9679662	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9749783	0.84[EUR][1000 genomes]
rs9973551	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv869668	chr2:40141079-40249854	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv873899	chr2:40161168-40281964	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1009532	chr2:40165606-40291224	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv535653	chr2:40165606-40291224	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873900	chr2:40202505-40278909	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv962063	chr2:40205436-40263295	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv873901	chr2:40207338-40264861	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40247200-40249200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:40247800-40255200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:40248200-40251200	ZNF genes & repeats	Dnd41	blood

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