Variant report

Variant	rs2102270
Chromosome Location	chr2:98955040-98955041
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	CBX3	chr2:98954687-98955075	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
ENSG00000222000	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10172281	0.96[ASN][1000 genomes]
rs10181000	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10190679	0.98[ASN][1000 genomes]
rs10199476	0.87[CHB][hapmap]
rs10210685	0.98[ASN][1000 genomes]
rs11124096	0.87[CHB][hapmap]
rs11124107	0.87[CHB][hapmap]
rs11673807	0.87[CHB][hapmap]
rs11679920	0.87[CHB][hapmap]
rs11889349	0.87[CHB][hapmap]
rs11895654	0.87[CHB][hapmap]
rs12478763	0.87[CHB][hapmap]
rs12622324	0.87[CHB][hapmap]
rs12999985	0.87[CHB][hapmap]
rs13014142	0.87[CHB][hapmap]
rs13394706	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13408372	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13415414	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13427344	1.00[ASN][1000 genomes]
rs13428221	0.91[ASN][1000 genomes]
rs13432099	0.98[ASN][1000 genomes]
rs1451251	0.93[CHB][hapmap]
rs1466944	0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs17429208	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2055591	0.98[ASN][1000 genomes]
rs2122756	0.87[CHB][hapmap]
rs2202387	0.87[CHB][hapmap]
rs2221416	0.87[CHB][hapmap]
rs2292118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2292119	0.87[CHB][hapmap]
rs4374424	0.87[CHB][hapmap]
rs4455212	0.92[CHB][hapmap]
rs4477970	0.87[CHB][hapmap]
rs4479470	0.87[CHB][hapmap]
rs4608580	0.87[CHB][hapmap]
rs4632400	0.87[CHB][hapmap]
rs4851935	0.87[CHB][hapmap]
rs4851951	0.91[CHB][hapmap]
rs56320609	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60924437	0.99[ASN][1000 genomes]
rs62156263	0.99[ASN][1000 genomes]
rs62156264	0.99[ASN][1000 genomes]
rs6543419	0.87[CHB][hapmap]
rs6715989	0.87[CHB][hapmap];0.82[MEX][hapmap]
rs6725543	0.87[CHB][hapmap];0.85[MEX][hapmap]
rs6747344	0.87[CHB][hapmap]
rs6747410	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs6754222	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72819909	0.98[ASN][1000 genomes]
rs7571001	1.00[ASN][1000 genomes]
rs7571110	1.00[ASN][1000 genomes]
rs7578802	0.87[CHB][hapmap]
rs7580008	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7586663	1.00[ASN][1000 genomes]
rs7601049	0.87[CHB][hapmap]
rs7606220	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008645	chr2:98915767-99010743	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1010466	chr2:98938886-98998109	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1013617	chr2:98943377-99004173	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2102270	TMEM127	cis	parietal	SCAN
rs2102270	ANKRD39	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98950800-98956000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:98951800-98959000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:98952000-98956200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:98952200-98956200	Weak transcription	H1 Cell Line	embryonic stem cell

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