Variant report

Variant	rs4494268
Chromosome Location	chr11:47038220-47038221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:46867290..46869103-chr11:47036825..47039117,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175216	Chromatin interaction
ENSG00000247675	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10501319	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs10769225	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10769226	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10769227	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10769228	0.98[ASN][1000 genomes]
rs10769234	0.82[CHB][hapmap]
rs10838624	1.00[AFR][1000 genomes]
rs10838635	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10838640	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10838641	0.98[ASN][1000 genomes]
rs10838644	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10838646	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10838652	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs10838658	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10838662	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs10838663	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[ASN][1000 genomes]
rs10838664	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11039002	0.91[MEX][hapmap];0.88[TSI][hapmap]
rs11039024	0.82[EUR][1000 genomes]
rs11039028	0.90[ASN][1000 genomes]
rs11039033	0.93[ASN][1000 genomes]
rs11039035	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039057	0.92[ASN][1000 genomes]
rs11039074	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs11039080	0.89[ASN][1000 genomes]
rs11039081	0.90[ASN][1000 genomes]
rs11600292	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[ASN][1000 genomes]
rs11601798	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11602250	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11603373	0.84[ASN][1000 genomes]
rs11606992	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11608083	0.93[ASN][1000 genomes]
rs12417519	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs12574410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17790204	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2087215	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[ASN][1000 genomes]
rs2279438	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2279439	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs2290883	1.00[AFR][1000 genomes]
rs2306028	0.82[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes]
rs2306033	0.82[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes]
rs2306036	0.90[GIH][hapmap];0.94[TSI][hapmap]
rs2306037	0.82[EUR][1000 genomes]
rs34340483	0.92[ASN][1000 genomes]
rs3922684	0.87[ASN][1000 genomes]
rs4269876	0.87[ASN][1000 genomes]
rs4315028	0.90[ASN][1000 genomes]
rs4394802	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4498951	0.87[ASN][1000 genomes]
rs4528282	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4548577	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4576779	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4581406	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4587689	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs4752815	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[ASN][1000 genomes]
rs4752816	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[ASN][1000 genomes]
rs4752946	0.82[GIH][hapmap];0.88[TSI][hapmap]
rs4752947	1.00[AFR][1000 genomes]
rs4752951	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4752965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4752969	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs58389391	1.00[AFR][1000 genomes]
rs61896133	0.87[ASN][1000 genomes]
rs61896136	0.87[ASN][1000 genomes]
rs6485715	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6485716	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6485726	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs7108822	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7111270	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7112854	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs7114683	0.92[ASN][1000 genomes]
rs7123632	0.96[ASN][1000 genomes]
rs7124648	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7126005	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7127741	0.92[ASN][1000 genomes]
rs7128193	0.93[ASN][1000 genomes]
rs7128650	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7130006	0.95[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7130947	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7929688	0.95[ASN][1000 genomes]
rs7935346	1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7937410	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7938169	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7939786	0.95[ASN][1000 genomes]
rs7940240	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7940441	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs7945558	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7946739	0.92[ASN][1000 genomes]
rs7950753	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[ASN][1000 genomes]
rs7951979	0.83[ASN][1000 genomes]
rs901747	0.83[ASN][1000 genomes]
rs923324	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[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	esv1805201	chr11:46971012-47063429	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv1819852	chr11:46971012-47064542	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4494268	PTPMT1	cis	parietal	SCAN
rs4494268	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs4494268	ACP2	cis	lymphoblastoid	seeQTL
rs4494268	DDB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47026600-47042200	Weak transcription	Small Intestine	intestine
2	chr11:47026800-47041000	Weak transcription	Hela-S3	cervix
3	chr11:47026800-47080200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:47027000-47040000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:47027200-47042000	Weak transcription	Brain Hippocampus Middle	brain
6	chr11:47027400-47039600	Weak transcription	Osteobl	bone
7	chr11:47027400-47056000	Weak transcription	Fetal Intestine Small	intestine
8	chr11:47027800-47048000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:47033000-47042000	Weak transcription	Fetal Lung	lung

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