Variant report

Variant	rs13149083
Chromosome Location	chr4:48809945-48809946
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	chr4:48809818..48813229-chr4:48833002..48835845,3	MCF-7	breast:
2	chr4:48809307..48810887-chr4:48829493..48831346,2	K562	blood:

Variant related genes	Relation type
ENSG00000109180	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10049761	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[MEX][hapmap];0.85[YRI][hapmap]
rs10938537	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs11727343	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11729065	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11733534	0.88[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.80[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11734191	0.86[ASN][1000 genomes]
rs11737677	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[MEX][hapmap];0.81[YRI][hapmap]
rs12504699	0.86[JPT][hapmap]
rs12512637	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12641022	0.84[ASN][1000 genomes]
rs13109500	0.83[ASN][1000 genomes]
rs13119041	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs13141838	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13142540	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes]
rs13152270	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1517674	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1554256	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes]
rs1589107	0.80[AMR][1000 genomes]
rs1876469	0.88[CEU][hapmap];0.82[CHB][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.92[YRI][hapmap]
rs2056201	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2085292	0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.96[YRI][hapmap]
rs2102397	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[MEX][hapmap]
rs2247481	0.80[LWK][hapmap];0.81[YRI][hapmap]
rs2289065	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2290516	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2354348	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[MEX][hapmap]
rs2572345	0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs2572350	0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2712156	0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2712157	0.89[ASN][1000 genomes]
rs2712158	0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs2712159	0.88[ASN][1000 genomes]
rs2883562	0.87[ASN][1000 genomes]
rs34730980	0.81[ASN][1000 genomes]
rs3761729	0.88[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4694904	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4694906	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4695407	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6447666	0.84[GIH][hapmap]
rs6825639	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6843340	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs7654032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660206	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.90[MEX][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs7665209	0.87[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7667288	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[MEX][hapmap];0.81[YRI][hapmap]
rs7687992	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9291326	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9637562	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9997920	0.88[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13149083	OCIAD2	cis	multi-tissue	Pritchard
rs13149083	MGC45416	cis	multi-tissue	Pritchard
rs13149083	OCIAD2	cis	cerebellum	SCAN
rs13149083	OCIAD2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48804600-48810000	Weak transcription	GM12878-XiMat	blood

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