Variant report

Variant	rs10811629
Chromosome Location	chr9:21840298-21840299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10114559	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs10119568	0.85[ASN][1000 genomes]
rs10119693	0.84[ASN][1000 genomes]
rs10121449	0.94[ASN][1000 genomes]
rs10738601	0.86[ASN][1000 genomes]
rs10757257	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs10811623	0.89[ASN][1000 genomes]
rs10811625	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs10811626	0.94[ASN][1000 genomes]
rs10965128	0.82[ASN][1000 genomes]
rs10965134	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10965135	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs10965141	0.88[ASN][1000 genomes]
rs10965143	1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs10965144	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs10965145	0.90[ASN][1000 genomes]
rs10965153	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11523031	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11532907	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12554745	0.81[AFR][1000 genomes]
rs1345020	0.81[ASN][1000 genomes]
rs1345023	0.81[ASN][1000 genomes]
rs1345024	0.81[ASN][1000 genomes]
rs1414243	0.91[CHB][hapmap];0.80[TSI][hapmap]
rs2165409	0.91[CHB][hapmap]
rs3900787	0.81[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs3922992	1.00[CHB][hapmap];0.84[YRI][hapmap];0.94[ASN][1000 genomes]
rs4454372	0.82[AFR][1000 genomes]
rs4615669	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs4636295	0.89[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4977567	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977733	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4977734	0.89[ASW][hapmap];0.82[LWK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs58377678	0.84[ASN][1000 genomes]
rs62556497	0.90[AFR][1000 genomes]
rs7022754	0.83[ASN][1000 genomes]
rs7023329	1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs7023954	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs7047826	0.90[AFR][1000 genomes]
rs7049092	0.83[ASN][1000 genomes]
rs7850937	0.89[ASW][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];0.87[AFR][1000 genomes]
rs7851133	0.89[ASW][hapmap];0.84[GIH][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7863090	0.94[ASN][1000 genomes]
rs7863942	0.81[ASN][1000 genomes]
rs7868783	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10811629	MTAP	cis	parietal	SCAN
rs10811629	IFNA21	cis	parietal	SCAN
rs10811629	MTAP	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21806600-21841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:21814400-21845200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:21817800-21840600	Weak transcription	Colonic Mucosa	Colon
4	chr9:21818600-21840800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:21818800-21840400	Weak transcription	Right Ventricle	heart
6	chr9:21819400-21840400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr9:21819400-21841600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:21823800-21840400	Strong transcription	Fetal Muscle Leg	muscle
9	chr9:21824200-21840400	Strong transcription	Fetal Lung	lung
10	chr9:21825000-21840600	Strong transcription	Dnd41	blood
11	chr9:21825000-21841800	Strong transcription	Primary T cells from cord blood	blood
12	chr9:21825000-21841800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr9:21825200-21840800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr9:21825200-21841400	Strong transcription	Fetal Thymus	thymus
15	chr9:21825200-21842200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:21825400-21840400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:21825400-21840600	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr9:21825800-21840600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:21825800-21840600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:21826000-21840800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr9:21831000-21840600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:21831800-21842000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr9:21832200-21840400	Strong transcription	Ovary	ovary
24	chr9:21832200-21842000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr9:21832200-21852400	Weak transcription	Stomach Mucosa	stomach
26	chr9:21832400-21840600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:21832400-21841800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr9:21832600-21841200	Weak transcription	Fetal Heart	heart
29	chr9:21833000-21841800	Strong transcription	Brain Hippocampus Middle	brain
30	chr9:21833000-21842000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr9:21833400-21842000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr9:21833600-21841800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:21833600-21841800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:21833800-21840400	Weak transcription	Gastric	stomach
35	chr9:21833800-21842000	Strong transcription	Liver	Liver
36	chr9:21833800-21843200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:21834600-21841200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr9:21835400-21840600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr9:21836000-21842000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr9:21836600-21842200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:21836800-21841800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:21837000-21840600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:21837000-21841200	Weak transcription	Brain Angular Gyrus	brain
44	chr9:21837000-21843600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:21837200-21840600	Strong transcription	Fetal Stomach	stomach
46	chr9:21837200-21841400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:21837200-21842000	Strong transcription	Left Ventricle	heart
48	chr9:21837200-21842000	ZNF genes & repeats	GM12878-XiMat	blood
49	chr9:21837200-21844600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:21837200-21850400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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