Variant report

Variant	rs4752872
Chromosome Location	chr11:47853795-47853796
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	chr11:47853054..47855600-chr11:47864603..47866811,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11039387	0.98[ASN][1000 genomes]
rs11819979	0.92[ASN][1000 genomes]
rs11820480	0.95[ASN][1000 genomes]
rs1474056	0.80[ASN][1000 genomes]
rs17198607	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs17791016	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs1872167	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2138767	0.81[ASN][1000 genomes]
rs2305982	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305983	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2869531	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869532	0.88[ASN][1000 genomes]
rs4752786	0.81[ASN][1000 genomes]
rs4752791	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[ASN][1000 genomes]
rs4752871	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752877	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4752879	0.93[ASN][1000 genomes]
rs57436966	0.92[ASN][1000 genomes]
rs58357937	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59205786	0.94[ASN][1000 genomes]
rs59652089	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60515486	0.85[ASN][1000 genomes]
rs6485772	0.87[ASN][1000 genomes]
rs6485774	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6485783	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6485784	1.00[ASN][1000 genomes]
rs6485788	0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7120737	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs7121264	0.88[ASN][1000 genomes]
rs7124949	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7924699	0.94[ASN][1000 genomes]
rs7927611	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931089	0.80[ASN][1000 genomes]
rs7942031	0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7945911	0.83[ASN][1000 genomes]
rs7946766	1.00[CEU][hapmap]
rs7952204	0.90[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
4	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv1049835	chr11:47837089-47928822	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv541036	chr11:47837089-47928822	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4752872	PTPMT1	cis	parietal	SCAN
rs4752872	ATG13	cis	parietal	SCAN
rs4752872	LOC441601	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47790200-47869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47795400-47866600	Strong transcription	Fetal Thymus	thymus
3	chr11:47795400-47868400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:47796200-47867400	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr11:47796200-47868200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:47796200-47868200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr11:47796200-47868400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:47796200-47868400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:47796200-47868600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:47796400-47858800	Strong transcription	Liver	Liver
11	chr11:47796400-47867600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:47796600-47868600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr11:47798000-47868000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:47798400-47864800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:47807000-47865600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr11:47820000-47864800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr11:47823000-47854600	Weak transcription	Fetal Heart	heart
18	chr11:47823200-47854800	Weak transcription	Aorta	Aorta
19	chr11:47831800-47868000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:47833800-47854600	Weak transcription	Esophagus	oesophagus
21	chr11:47834200-47854000	Weak transcription	Right Ventricle	heart
22	chr11:47834200-47855200	Weak transcription	Psoas Muscle	Psoas
23	chr11:47834600-47856000	Weak transcription	Colonic Mucosa	Colon
24	chr11:47835400-47854000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:47837200-47857200	Weak transcription	Small Intestine	intestine
26	chr11:47837800-47854000	Weak transcription	NHEK	skin
27	chr11:47840000-47854000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:47840600-47854000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr11:47840600-47863600	Weak transcription	Stomach Mucosa	stomach
30	chr11:47842600-47854000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr11:47843400-47854000	Weak transcription	Brain Angular Gyrus	brain
32	chr11:47843400-47854000	Weak transcription	Brain Hippocampus Middle	brain
33	chr11:47843400-47854800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:47843400-47855200	Weak transcription	Pancreas	Pancrea
35	chr11:47843600-47853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr11:47843600-47854000	Weak transcription	HMEC	breast
37	chr11:47843800-47854000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr11:47843800-47854000	Weak transcription	NHDF-Ad	bronchial
39	chr11:47845000-47853800	Weak transcription	NH-A	brain
40	chr11:47845000-47854000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr11:47845200-47854000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:47845200-47854000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr11:47845200-47854000	Weak transcription	HSMMtube	muscle
44	chr11:47845200-47854200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:47845200-47854800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr11:47845400-47854000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:47846600-47864200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr11:47846600-47867000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:47847000-47868200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:47847200-47867400	Strong transcription	Rectal Mucosa Donor 29	rectum

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