Variant report

Variant	rs10757257
Chromosome Location	chr9:21806564-21806565
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	chr9:21805334..21807056-chr9:22107638..22109490,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10114559	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10119568	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10119693	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10121449	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10121899	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10738598	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10738601	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757244	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10811603	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10811608	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10811623	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10811625	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10811626	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10811629	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs10965117	0.80[AMR][1000 genomes]
rs10965128	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10965133	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10965134	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10965135	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10965141	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10965143	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10965144	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10965145	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10965153	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11523031	0.88[ASN][1000 genomes]
rs11532907	0.81[ASN][1000 genomes]
rs12555601	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13298275	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1335503	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1335510	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1335511	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1341866	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1345020	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1345023	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1345024	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1414243	0.90[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1414253	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1561650	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2165409	0.89[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3900787	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3922992	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4265275	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4364717	0.96[CEU][hapmap];0.82[GIH][hapmap]
rs4615669	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4977567	0.87[ASN][1000 genomes]
rs4977733	0.88[ASN][1000 genomes]
rs58377678	0.88[ASN][1000 genomes]
rs7022754	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7023329	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs7023954	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7029036	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7033879	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7038523	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7049092	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7850937	0.83[GIH][hapmap]
rs7851133	0.83[GIH][hapmap]
rs7863090	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7863942	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7868783	0.88[ASN][1000 genomes]
rs958219	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1026981	chr9:21748202-21811697	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
3	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10757257	MTAP	cis	multi-tissue	Pritchard
rs10757257	MTAP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21803600-21808200	Weak transcription	Aorta	Aorta
2	chr9:21804000-21806600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr9:21804000-21807400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr9:21804000-21808800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:21804000-21810800	Weak transcription	Right Ventricle	heart
6	chr9:21804000-21814200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr9:21804000-21817600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:21804000-21838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr9:21804200-21806600	Weak transcription	Right Atrium	heart
10	chr9:21804200-21806800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr9:21804200-21806800	Enhancers	Colon Smooth Muscle	Colon
12	chr9:21804200-21807400	Weak transcription	Thymus	Thymus
13	chr9:21804200-21810800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:21804200-21813200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr9:21804200-21813200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:21804400-21808800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr9:21804400-21808800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr9:21804400-21813200	Weak transcription	Colonic Mucosa	Colon
19	chr9:21804400-21816000	Weak transcription	Fetal Kidney	kidney
20	chr9:21804600-21806800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:21804600-21807800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:21804600-21808200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:21804600-21810400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:21804800-21806600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:21804800-21806800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:21804800-21808000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:21804800-21813600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr9:21805000-21806600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr9:21805000-21806600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr9:21805000-21806600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr9:21805000-21806800	Enhancers	Brain Germinal Matrix	brain
32	chr9:21805000-21807200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:21805000-21807200	Weak transcription	Primary B cells from cord blood	blood
34	chr9:21805000-21807400	Enhancers	Ovary	ovary
35	chr9:21805000-21807600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:21805000-21808200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr9:21805000-21808200	Weak transcription	Liver	Liver
38	chr9:21805000-21809000	Weak transcription	Adipose Nuclei	Adipose
39	chr9:21805000-21809000	Weak transcription	HSMMtube	muscle
40	chr9:21805000-21809800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:21805000-21809800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:21805000-21809800	Weak transcription	NHDF-Ad	bronchial
43	chr9:21805000-21810800	Weak transcription	Brain Anterior Caudate	brain
44	chr9:21805000-21811200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:21805000-21812000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:21805000-21813200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr9:21805000-21816200	Weak transcription	Fetal Brain Male	brain
48	chr9:21805200-21806600	Genic enhancers	H1 Cell Line	embryonic stem cell
49	chr9:21805200-21806600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:21805200-21806600	Genic enhancers	HUES64 Cell Line	embryonic stem cell

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