Variant report

Variant	rs4607709
Chromosome Location	chr9:21881338-21881339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10117550	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10118406	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10965174	0.83[CEU][hapmap]
rs1134871	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11526324	0.83[CEU][hapmap]
rs11531716	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12553901	0.83[CEU][hapmap]
rs1418072	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2027484	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3928893	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4352938	0.83[CEU][hapmap]
rs4593639	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4607704	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4977569	0.83[CEU][hapmap]
rs4977737	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4977738	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977739	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6475592	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]
rs7028211	0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4607709	MTAP	cis	Frontal Cortex	GTEx
rs4607709	MTAP	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21857400-21883800	Weak transcription	Pancreas	Pancrea
2	chr9:21859000-21892000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr9:21862200-21886800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:21865000-21890200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:21865400-21892600	Weak transcription	Colonic Mucosa	Colon
6	chr9:21865600-21890000	Weak transcription	Placenta	Placenta
7	chr9:21865800-21882200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr9:21865800-21883200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:21865800-21886800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr9:21865800-21889600	Weak transcription	Ovary	ovary
11	chr9:21866000-21883800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:21866000-21886000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:21866000-21890200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:21866800-21883400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr9:21869000-21881600	Weak transcription	Lung	lung
16	chr9:21869000-21883600	Weak transcription	Aorta	Aorta
17	chr9:21869400-21889600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr9:21869600-21890000	Weak transcription	Thymus	Thymus
19	chr9:21870200-21889600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:21873000-21881800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr9:21873000-21893000	Weak transcription	NHDF-Ad	bronchial
22	chr9:21874200-21890200	Weak transcription	Osteobl	bone
23	chr9:21874400-21889600	Weak transcription	NHEK	skin
24	chr9:21874400-21893800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:21874800-21881400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:21879000-21881400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:21879400-21881600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:21879600-21881400	Strong transcription	HSMM	muscle
29	chr9:21879800-21881400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:21879800-21882000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:21879800-21883400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:21879800-21883400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr9:21879800-21884400	Weak transcription	HMEC	breast
34	chr9:21879800-21889400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:21880000-21886200	Weak transcription	Primary T cells from cord blood	blood
36	chr9:21880200-21881600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:21880200-21890600	Weak transcription	HUVEC	blood vessel
38	chr9:21880400-21883400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr9:21880400-21884200	Weak transcription	Dnd41	blood
40	chr9:21880400-21885600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:21880400-21888200	Weak transcription	Small Intestine	intestine
42	chr9:21880400-21889400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:21880400-21890200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:21880400-21890200	Weak transcription	Gastric	stomach
45	chr9:21880400-21890800	Weak transcription	NH-A	brain
46	chr9:21880400-21892600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr9:21880400-21901400	Weak transcription	HSMMtube	muscle
48	chr9:21880600-21883400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr9:21880600-21883600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:21880600-21886600	Weak transcription	Liver	Liver

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