Variant report

Variant	rs6542931
Chromosome Location	chr2:100958356-100958357
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	chr2:100952978..100954595-chr2:100957263..100960218,2	MCF-7	breast:
2	chr2:100937601..100941206-chr2:100954662..100959386,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10167159	1.00[ASN][1000 genomes]
rs10180570	0.88[ASN][1000 genomes]
rs10184899	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10193535	0.88[ASN][1000 genomes]
rs10198495	1.00[ASN][1000 genomes]
rs10198682	1.00[ASN][1000 genomes]
rs10200480	1.00[ASN][1000 genomes]
rs10201098	1.00[ASN][1000 genomes]
rs10204833	1.00[ASN][1000 genomes]
rs10206374	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10208900	1.00[ASN][1000 genomes]
rs10208911	1.00[ASN][1000 genomes]
rs10209186	1.00[ASN][1000 genomes]
rs1107429	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391930	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13396147	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13404823	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407408	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407648	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407891	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13410582	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13419808	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13420942	1.00[ASN][1000 genomes]
rs1347721	0.88[ASN][1000 genomes]
rs1370627	1.00[ASN][1000 genomes]
rs1437970	1.00[ASN][1000 genomes]
rs17023985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024129	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024136	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024144	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1898571	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1898574	1.00[ASN][1000 genomes]
rs2309793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55640826	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55843950	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56051859	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56118658	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56342384	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56656536	0.88[ASN][1000 genomes]
rs58876304	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60131548	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60609848	0.88[ASN][1000 genomes]
rs60898093	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61321970	1.00[ASN][1000 genomes]
rs6542932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542939	1.00[ASN][1000 genomes]
rs6542941	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708942	0.88[ASN][1000 genomes]
rs6713862	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6714109	1.00[ASN][1000 genomes]
rs6716009	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6716367	0.88[ASN][1000 genomes]
rs6724695	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6732285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739576	1.00[ASN][1000 genomes]
rs6740098	1.00[ASN][1000 genomes]
rs6750866	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754379	1.00[ASN][1000 genomes]
rs6755395	1.00[ASN][1000 genomes]
rs6757774	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6758156	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6758161	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6758515	0.88[ASN][1000 genomes]
rs6761561	0.88[ASN][1000 genomes]
rs72960172	1.00[ASN][1000 genomes]
rs72960184	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72960186	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72960202	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73966107	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73966108	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73968412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73968415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73968817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556717	1.00[ASN][1000 genomes]
rs7557137	1.00[ASN][1000 genomes]
rs7559939	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7559946	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562461	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562479	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562486	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562615	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7564178	0.88[ASN][1000 genomes]
rs7572119	0.88[ASN][1000 genomes]
rs7574684	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7576749	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582546	1.00[EUR][1000 genomes]
rs7585898	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7587333	0.88[ASN][1000 genomes]
rs7597631	1.00[ASN][1000 genomes]
rs7597722	1.00[ASN][1000 genomes]
rs7606723	1.00[ASN][1000 genomes]
rs9308834	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100956800-100967200	Weak transcription	Gastric	stomach

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