Variant report

Variant	rs72960186
Chromosome Location	chr2:100988972-100988973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:100987392-100992126	K562	blood:	n/a	n/a
2	SETDB1	chr2:100988062-100989035	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100936704..100939882-chr2:100988409..100992590,4	MCF-7	breast:
2	chr2:100987418..100989258-chr2:100992351..100994507,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269383	TF binding region
ENSG00000270699	TF binding region
ENSG00000170500	Chromatin interaction
ENSG00000270699	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10167159	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10180570	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10184899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193535	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10198495	0.88[ASN][1000 genomes]
rs10198682	0.88[ASN][1000 genomes]
rs10200480	0.88[ASN][1000 genomes]
rs10201098	0.88[ASN][1000 genomes]
rs10204833	0.88[ASN][1000 genomes]
rs10206374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208900	0.88[ASN][1000 genomes]
rs10208911	0.88[ASN][1000 genomes]
rs10209186	0.88[ASN][1000 genomes]
rs1057056	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1057063	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1107429	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1124009	0.86[AMR][1000 genomes]
rs13391930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13396147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407408	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410582	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419808	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420942	0.88[ASN][1000 genomes]
rs1347721	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1370627	0.88[ASN][1000 genomes]
rs1437970	0.88[ASN][1000 genomes]
rs17023985	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024035	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024129	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024136	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024144	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024209	0.86[AMR][1000 genomes]
rs1898571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898574	0.88[ASN][1000 genomes]
rs2309793	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3748936	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4149506	0.81[AMR][1000 genomes]
rs4149509	0.81[AMR][1000 genomes]
rs4149514	0.83[AMR][1000 genomes]
rs4149515	0.86[AMR][1000 genomes]
rs55640826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55843950	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051859	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56118658	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56342384	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56656536	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56741959	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57862179	0.83[AMR][1000 genomes]
rs58164864	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58876304	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60131548	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60609848	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60898093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61321970	0.88[ASN][1000 genomes]
rs61710328	0.83[AMR][1000 genomes]
rs6542931	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6542932	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6542939	0.88[ASN][1000 genomes]
rs6542941	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6708942	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6713862	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714109	0.88[ASN][1000 genomes]
rs6716009	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716367	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6724695	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725672	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6732285	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6736938	0.81[AMR][1000 genomes]
rs6739576	0.88[ASN][1000 genomes]
rs6739589	0.90[AMR][1000 genomes]
rs6740098	0.88[ASN][1000 genomes]
rs6749572	0.81[AMR][1000 genomes]
rs6750866	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6754379	0.88[ASN][1000 genomes]
rs6754869	0.83[AMR][1000 genomes]
rs6755285	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6755395	0.88[ASN][1000 genomes]
rs6757774	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758156	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758161	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758515	1.00[ASN][1000 genomes]
rs6758622	0.83[AMR][1000 genomes]
rs6761561	1.00[ASN][1000 genomes]
rs72960172	0.88[ASN][1000 genomes]
rs72960184	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72960202	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73966107	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73966108	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73968412	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73968415	0.82[ASN][1000 genomes]
rs73968817	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7556717	0.88[ASN][1000 genomes]
rs7557137	0.88[ASN][1000 genomes]
rs7559939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561065	0.81[AMR][1000 genomes]
rs7562461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564178	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7572119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7574684	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576749	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582096	0.81[AMR][1000 genomes]
rs7582546	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7585713	0.81[AMR][1000 genomes]
rs7585898	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587333	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7596483	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7597631	0.88[ASN][1000 genomes]
rs7597722	0.88[ASN][1000 genomes]
rs7606723	0.88[ASN][1000 genomes]
rs9308834	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv874701	chr2:100976139-101023261	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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