Variant report

Variant	rs4636295
Chromosome Location	chr9:21854199-21854200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:21854180-21856002	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
MTAP	TF binding region

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

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

rs_ID	r²[population]
rs10811629	0.89[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10965161	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10965162	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10965164	0.96[CEU][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10965174	0.80[GIH][hapmap]
rs11523031	0.89[AFR][1000 genomes]
rs11526324	0.80[GIH][hapmap];0.80[MEX][hapmap]
rs12554745	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3802394	0.80[GIH][hapmap];0.84[MEX][hapmap]
rs3900787	0.82[YRI][hapmap]
rs3922992	0.84[YRI][hapmap]
rs4454372	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4977567	0.93[AFR][1000 genomes]
rs4977733	0.91[AFR][1000 genomes]
rs4977734	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4977736	0.80[GIH][hapmap]
rs62556496	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62556497	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7047826	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7850937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7851133	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7865071	0.80[GIH][hapmap]
rs7868783	0.90[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4636295	MTAP	cis	parietal	SCAN
rs4636295	ADAMTSL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21839400-21854400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:21841400-21858800	Weak transcription	Colonic Mucosa	Colon
3	chr9:21841600-21854200	Weak transcription	Hela-S3	cervix
4	chr9:21841600-21854400	Weak transcription	NHLF	lung
5	chr9:21841600-21854600	Weak transcription	NHDF-Ad	bronchial
6	chr9:21841600-21858400	Weak transcription	Spleen	Spleen
7	chr9:21841800-21854600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:21841800-21854800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:21841800-21854800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr9:21841800-21855400	Weak transcription	Gastric	stomach
11	chr9:21841800-21856200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:21841800-21856400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr9:21841800-21858600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr9:21841800-21864600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:21842000-21854600	Weak transcription	HSMMtube	muscle
16	chr9:21842000-21854600	Weak transcription	NHEK	skin
17	chr9:21842000-21854600	Weak transcription	Osteobl	bone
18	chr9:21842000-21855000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr9:21842000-21857800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr9:21842000-21858400	Weak transcription	Right Ventricle	heart
21	chr9:21846000-21854800	Weak transcription	Fetal Kidney	kidney
22	chr9:21846600-21869800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:21847600-21871600	Strong transcription	Dnd41	blood
24	chr9:21847800-21854200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:21848000-21869600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr9:21848200-21856200	Strong transcription	Primary T cells from cord blood	blood
27	chr9:21848400-21854200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr9:21848800-21854200	Weak transcription	Thymus	Thymus
29	chr9:21848800-21854200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr9:21848800-21854600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr9:21848800-21854600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:21848800-21854600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr9:21848800-21854800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:21848800-21861400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr9:21848800-21866000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:21849000-21854200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr9:21849000-21854200	Weak transcription	Placenta	Placenta
38	chr9:21849000-21854200	Weak transcription	Left Ventricle	heart
39	chr9:21849000-21854200	Weak transcription	Psoas Muscle	Psoas
40	chr9:21849000-21854400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr9:21849000-21854400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr9:21849000-21854600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:21849000-21854800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr9:21849000-21854800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr9:21849000-21854800	Weak transcription	Brain Substantia Nigra	brain
46	chr9:21849000-21854800	Weak transcription	Fetal Brain Male	brain
47	chr9:21849000-21854800	Weak transcription	HSMM	muscle
48	chr9:21849000-21855000	Weak transcription	Fetal Lung	lung
49	chr9:21849000-21855400	Weak transcription	Lung	lung
50	chr9:21849000-21856200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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