Variant report

Variant	rs6475592
Chromosome Location	chr9:21865842-21865843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10117550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118406	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10965174	0.83[CEU][hapmap]
rs1134871	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11526324	0.83[CEU][hapmap]
rs11531716	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12553901	0.83[CEU][hapmap]
rs1418072	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs15735	0.80[AMR][1000 genomes]
rs2027484	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3928893	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4352938	0.83[CEU][hapmap]
rs4593639	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4607704	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4607709	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977569	0.83[CEU][hapmap]
rs4977737	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4977738	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977739	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7028211	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7047648	0.82[GIH][hapmap]
rs756641	0.83[CEU][hapmap]
rs7865071	0.83[CEU][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	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	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
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6475592	MTAP	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21846600-21869800	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr9:21847600-21871600	Strong transcription	Dnd41	blood
3	chr9:21848000-21869600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:21848800-21866000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:21849000-21868200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr9:21849000-21870000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:21849000-21870200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:21849200-21866200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:21851400-21866800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:21852600-21866000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:21853800-21866800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:21854200-21866000	Strong transcription	Adipose Nuclei	Adipose
13	chr9:21854200-21870200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:21854400-21866000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:21854400-21866200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:21854400-21869800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:21854600-21866400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:21854600-21867000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:21854800-21866400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:21855400-21873000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr9:21855600-21879800	Weak transcription	Small Intestine	intestine
22	chr9:21855800-21868600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:21855800-21870600	Strong transcription	HMEC	breast
24	chr9:21856600-21871200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:21857000-21871200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:21857200-21866200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:21857400-21883800	Weak transcription	Pancreas	Pancrea
28	chr9:21858200-21866200	Strong transcription	HSMM	muscle
29	chr9:21859000-21892000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr9:21860200-21879800	Weak transcription	Right Ventricle	heart
31	chr9:21860400-21867200	Weak transcription	Brain Angular Gyrus	brain
32	chr9:21860400-21867200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:21860400-21868600	Weak transcription	Thymus	Thymus
34	chr9:21862200-21886800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr9:21862400-21874200	Weak transcription	Fetal Heart	heart
36	chr9:21863200-21866000	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr9:21863200-21880800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr9:21863400-21866000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr9:21863800-21866000	Strong transcription	Primary B cells from cord blood	blood
40	chr9:21863800-21866000	Strong transcription	Fetal Lung	lung
41	chr9:21863800-21866200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr9:21863800-21867000	Strong transcription	NHEK	skin
43	chr9:21863800-21869800	Strong transcription	NH-A	brain
44	chr9:21863800-21870600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:21864000-21866200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:21864200-21866600	Strong transcription	Hela-S3	cervix
47	chr9:21864200-21868400	Weak transcription	NHDF-Ad	bronchial
48	chr9:21864200-21870000	Weak transcription	HUVEC	blood vessel
49	chr9:21864200-21870200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:21864200-21872000	Weak transcription	Stomach Mucosa	stomach

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