Variant report

Variant	rs10507186
Chromosome Location	chr12:105290449-105290450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105277401..105280097-chr12:105289750..105292051,2	MCF-7	breast:
2	chr12:105289655..105291456-chr12:105306403..105308670,2	MCF-7	breast:
3	chr12:105290364..105293204-chr12:105349716..105351702,2	MCF-7	breast:
4	chr12:105289003..105291850-chr12:105292916..105295030,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10161522	0.91[EUR][1000 genomes]
rs10507187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10507188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112218	1.00[CEU][hapmap]
rs11112276	0.91[EUR][1000 genomes]
rs11112277	0.91[EUR][1000 genomes]
rs11112279	0.91[EUR][1000 genomes]
rs11112283	0.86[EUR][1000 genomes]
rs11112303	0.83[EUR][1000 genomes]
rs11112307	0.85[EUR][1000 genomes]
rs11112346	0.81[GIH][hapmap]
rs11503466	0.85[EUR][1000 genomes]
rs12296144	0.88[EUR][1000 genomes]
rs12299385	0.85[EUR][1000 genomes]
rs12299936	0.91[EUR][1000 genomes]
rs12300005	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[EUR][1000 genomes]
rs12301432	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[EUR][1000 genomes]
rs12301850	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs12306191	0.91[EUR][1000 genomes]
rs12306443	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes]
rs12306848	1.00[CEU][hapmap]
rs12308952	0.91[EUR][1000 genomes]
rs12309588	0.88[CHB][hapmap]
rs12310790	0.85[EUR][1000 genomes]
rs12313077	0.91[EUR][1000 genomes]
rs12314995	0.91[EUR][1000 genomes]
rs12315975	0.91[EUR][1000 genomes]
rs12315983	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12316001	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12319632	0.91[EUR][1000 genomes]
rs12320024	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes]
rs12320195	0.91[EUR][1000 genomes]
rs12320880	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12321224	0.91[EUR][1000 genomes]
rs12321226	0.91[EUR][1000 genomes]
rs12321381	1.00[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs17036439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17036463	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17036494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17036558	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17041531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35879768	0.91[EUR][1000 genomes]
rs3812795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816923	0.88[CHB][hapmap];1.00[YRI][hapmap]
rs3935722	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4077312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4268581	0.91[EUR][1000 genomes]
rs4357778	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4375513	1.00[CEU][hapmap]
rs4553438	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs58005679	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58115870	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58447363	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58483223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60057011	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60096703	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60310033	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60809012	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60956548	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61638859	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7131977	1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[EUR][1000 genomes]
rs7299019	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs7303898	0.81[EUR][1000 genomes]
rs73383412	0.81[EUR][1000 genomes]
rs73387265	0.83[EUR][1000 genomes]
rs7960890	0.81[EUR][1000 genomes]
rs7960937	0.81[EUR][1000 genomes]
rs7970504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971575	0.88[CHB][hapmap]
rs7975754	0.81[EUR][1000 genomes]
rs7975836	0.81[EUR][1000 genomes]
rs9738733	0.83[EUR][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	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	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10507186	SYPL2	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105275400-105297000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:105278400-105293200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:105278600-105313800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:105284600-105309000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:105285000-105296200	Weak transcription	Aorta	Aorta
6	chr12:105289000-105290600	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr12:105289000-105290600	Enhancers	Hela-S3	cervix
8	chr12:105289000-105290600	Enhancers	HepG2	liver
9	chr12:105289800-105290800	Flanking Active TSS	Liver	Liver
10	chr12:105289800-105290800	Enhancers	Stomach Mucosa	stomach
11	chr12:105290200-105290800	Enhancers	A549	lung
12	chr12:105290400-105290800	Enhancers	Gastric	stomach
13	chr12:105290400-105290800	Enhancers	Pancreas	Pancrea
14	chr12:105290400-105292600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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