Variant report

Variant	rs2063800
Chromosome Location	chr2:123835795-123835796
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:123828454..123831297-chr2:123833230..123835913,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232740	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10178398	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10496606	0.89[CEU][hapmap];0.81[AMR][1000 genomes]
rs10864884	0.82[AMR][1000 genomes]
rs11122938	0.82[AMR][1000 genomes]
rs1154994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1154995	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1154996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1154997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1160011	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1160012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694990	0.88[CEU][hapmap]
rs11900012	0.80[AMR][1000 genomes]
rs11903864	0.87[AFR][1000 genomes]
rs12466984	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12476143	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12477691	0.82[AMR][1000 genomes]
rs12478792	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478793	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12620936	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12996298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12997587	0.82[AMR][1000 genomes]
rs13010429	0.82[AMR][1000 genomes]
rs13010613	0.82[AMR][1000 genomes]
rs13031371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13033509	0.82[AMR][1000 genomes]
rs13033663	0.82[AMR][1000 genomes]
rs13033813	0.82[AMR][1000 genomes]
rs1395931	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1515164	0.80[AMR][1000 genomes]
rs1515165	0.82[AMR][1000 genomes]
rs1515166	0.82[AMR][1000 genomes]
rs1605496	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs1605497	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs1605498	0.89[CEU][hapmap];0.80[MEX][hapmap];0.82[AMR][1000 genomes]
rs1605499	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs1606802	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17368634	0.82[AMR][1000 genomes]
rs17381599	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17465799	0.82[AMR][1000 genomes]
rs17466105	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2244129	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2248895	0.98[ASN][1000 genomes]
rs2419069	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs2419071	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2458994	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661001	0.93[ASN][1000 genomes]
rs2661032	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661035	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2661036	0.95[ASN][1000 genomes]
rs2661041	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2661043	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2661044	0.93[ASN][1000 genomes]
rs2661045	0.93[ASN][1000 genomes]
rs2673185	0.81[EUR][1000 genomes]
rs2673187	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2673188	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2673189	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2673194	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2673196	0.92[ASN][1000 genomes]
rs2900804	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299536	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299539	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs299540	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs299544	0.85[CHD][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs299546	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299549	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299550	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299553	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299560	0.92[ASN][1000 genomes]
rs299561	0.97[ASN][1000 genomes]
rs35870013	0.82[AMR][1000 genomes]
rs4848824	0.96[ASN][1000 genomes]
rs62166501	0.87[AFR][1000 genomes]
rs62166527	0.85[AFR][1000 genomes]
rs6541877	0.80[AMR][1000 genomes]
rs6541878	0.82[AMR][1000 genomes]
rs67156328	0.82[AMR][1000 genomes]
rs6726973	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747893	0.81[EUR][1000 genomes]
rs6754344	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6755603	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6755929	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6756049	0.82[AMR][1000 genomes]
rs6761730	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7608420	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7608426	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7608772	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7609057	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs957759	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9636359	0.81[AMR][1000 genomes];0.95[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	nsv492280	chr2:123447662-123973577	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2760647	chr2:123678437-124619697	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1010200	chr2:123816326-123887210	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv961349	chr2:123827896-123840926	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2063800	CNTNAP5	cis	cerebellum	SCAN

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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