Variant report

Variant	rs13016127
Chromosome Location	chr2:234784117-234784118
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234784096..234785745-chr2:234791587..234793695,2	MCF-7	breast:
2	chr2:234783189..234785802-chr2:234814089..234815780,2	K562	blood:
3	chr2:234774817..234777725-chr2:234781987..234784412,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224287	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1003540	0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10166942	0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10170399	0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10187654	0.96[ASN][1000 genomes]
rs10929309	0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10929312	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11563063	0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11563066	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11563227	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11892538	0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12997802	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13016553	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1392606	0.96[CEU][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965629	0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1985366	0.92[ASN][1000 genomes]
rs213542	0.80[AMR][1000 genomes]
rs2159200	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286430	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286431	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2302155	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2362290	0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3732215	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4233636	0.83[ASN][1000 genomes]
rs4663983	0.93[ASN][1000 genomes]
rs4663986	0.83[ASN][1000 genomes]
rs6431643	0.83[GIH][hapmap]
rs6431648	0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs6709005	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs6738979	0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6760630	0.96[ASN][1000 genomes]
rs737636	0.84[ASN][1000 genomes]
rs7567475	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7604471	0.82[ASN][1000 genomes]
rs887061	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs917432	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs917433	0.89[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs917434	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs968402	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs990418	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13016127	ARL4C	cis	parietal	SCAN
rs13016127	NCL	cis	parietal	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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