Variant report

Variant	rs10117507
Chromosome Location	chr9:21864098-21864099
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	chr9:21863692-21864172	HUVEC	blood vessel:	n/a	n/a
2	FOSL1	chr9:21863704-21864166	HCT-116	colon:	n/a	n/a
3	ARID3A	chr9:21863551-21864126	HepG2	liver:	n/a	n/a
4	GATA2	chr9:21863276-21864100	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr9:21863464-21864235	PFSK-1	brain:	n/a	n/a
6	CHD2	chr9:21863919-21864140	GM12878	blood:	n/a	n/a
7	JUND	chr9:21863638-21864184	HCT-116	colon:	n/a	chr9:21863860-21863871
8	GATA3	chr9:21863546-21864129	SK-N-SH	brain:	n/a	n/a
9	FOS	chr9:21863671-21864161	HUVEC	blood vessel:	n/a	chr9:21863860-21863871
10	ESR1	chr9:21863711-21864159	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000265194	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10811635	0.87[TSI][hapmap]
rs10965165	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10965168	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10965174	0.90[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10965175	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11526324	0.90[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11531660	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11536713	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12236836	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12553901	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3802394	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4352938	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4587423	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4977569	0.90[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4977735	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4977736	0.86[CEU][hapmap];0.94[GIH][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4977742	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4977743	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4977744	0.83[EUR][1000 genomes]
rs4977745	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62556506	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62556519	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62556520	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7044807	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs756641	0.90[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7865071	0.90[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[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	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
rs10117507	MTAP	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21841800-21864600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:21846600-21869800	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:21847600-21871600	Strong transcription	Dnd41	blood
4	chr9:21848000-21869600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:21848800-21866000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:21849000-21864200	Weak transcription	Brain Germinal Matrix	brain
7	chr9:21849000-21865800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:21849000-21868200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr9:21849000-21870000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:21849000-21870200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:21849200-21866200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:21849600-21864600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:21851400-21866800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:21852600-21866000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:21853600-21864600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr9:21853800-21866800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:21854200-21865800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:21854200-21866000	Strong transcription	Adipose Nuclei	Adipose
19	chr9:21854200-21870200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr9:21854400-21866000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:21854400-21866200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:21854400-21869800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:21854600-21864600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr9:21854600-21866400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:21854600-21867000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:21854800-21866400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:21855400-21864400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr9:21855400-21873000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr9:21855600-21879800	Weak transcription	Small Intestine	intestine
30	chr9:21855800-21864200	Weak transcription	Fetal Brain Male	brain
31	chr9:21855800-21868600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:21855800-21870600	Strong transcription	HMEC	breast
33	chr9:21856600-21871200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:21856800-21864600	Weak transcription	Gastric	stomach
35	chr9:21857000-21871200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr9:21857200-21866200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:21857400-21883800	Weak transcription	Pancreas	Pancrea
38	chr9:21858200-21866200	Strong transcription	HSMM	muscle
39	chr9:21858800-21864400	Weak transcription	Esophagus	oesophagus
40	chr9:21859000-21864600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr9:21859000-21892000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr9:21859200-21864400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:21859200-21864400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:21859800-21864400	Weak transcription	Spleen	Spleen
45	chr9:21860000-21865400	Weak transcription	Colon Smooth Muscle	Colon
46	chr9:21860200-21879800	Weak transcription	Right Ventricle	heart
47	chr9:21860400-21864200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr9:21860400-21864400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr9:21860400-21864400	Weak transcription	Brain Anterior Caudate	brain
50	chr9:21860400-21864400	Weak transcription	Lung	lung

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