Variant report

Variant	rs1196883
Chromosome Location	chr12:105488141-105488142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105484191..105488176-chr12:105493160..105495554,3	MCF-7	breast:
2	chr12:105487341..105488977-chr12:105499330..105501677,2	K562	blood:
3	chr12:105486698..105489306-chr12:105500533..105503211,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136051	Chromatin interaction
ENSG00000257999	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10778366	0.89[ASN][1000 genomes]
rs10861327	0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs10861328	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10861329	0.90[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs10861330	0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10861331	0.89[ASN][1000 genomes]
rs10861332	0.89[ASN][1000 genomes]
rs10861333	0.89[ASN][1000 genomes]
rs10861335	0.95[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs10861336	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs11112347	0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs11112349	0.82[ASN][1000 genomes]
rs11112350	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11112351	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs11112352	0.89[ASN][1000 genomes]
rs11112356	0.89[ASN][1000 genomes]
rs11112414	0.82[CHD][hapmap]
rs11611105	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs11612252	0.94[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs11613233	0.87[ASN][1000 genomes]
rs11613261	0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1196751	0.84[CEU][hapmap]
rs1196766	0.84[CHD][hapmap]
rs1196767	0.84[CHD][hapmap]
rs1196804	0.86[CHD][hapmap]
rs1196812	0.88[CEU][hapmap]
rs1196814	0.84[CHD][hapmap]
rs1196816	0.88[CEU][hapmap]
rs1196827	0.81[CEU][hapmap]
rs1196836	0.83[CHD][hapmap]
rs1196840	0.88[CEU][hapmap]
rs1196865	0.84[CHD][hapmap]
rs1196879	0.99[ASN][1000 genomes]
rs1196880	0.99[ASN][1000 genomes]
rs1196882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1196886	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1201657	0.86[CHD][hapmap]
rs1201658	0.85[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap]
rs12367626	0.89[ASN][1000 genomes]
rs12581638	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs17242777	0.89[ASN][1000 genomes]
rs1732377	0.98[ASN][1000 genomes]
rs1732384	0.84[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap]
rs2374451	0.86[ASN][1000 genomes]
rs2440693	0.98[ASN][1000 genomes]
rs2440713	0.88[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap]
rs2440719	0.88[CEU][hapmap]
rs4144467	0.82[ASN][1000 genomes]
rs4144468	0.82[ASN][1000 genomes]
rs56118650	0.82[ASN][1000 genomes]
rs56188643	0.82[ASN][1000 genomes]
rs56369757	0.82[ASN][1000 genomes]
rs7308195	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7311691	0.89[ASN][1000 genomes]
rs73179949	0.89[ASN][1000 genomes]
rs7962686	0.85[ASN][1000 genomes]
rs9143	0.85[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1196883	LOC387882	cis	multi-tissue	Pritchard
rs1196883	APPL2	cis	cerebellum	SCAN
rs1196883	KIAA1033	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105487000-105488200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:105487000-105488600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:105487000-105488600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:105487000-105493200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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