Variant report

Variant	rs2165408
Chromosome Location	chr9:21802469-21802470
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	SP1	chr9:21802025-21802837	H1-hESC	embryonic stem cell:	n/a	chr9:21802621-21802630 chr9:21802623-21802636 chr9:21802518-21802525
2	MAX	chr9:21802218-21803556	HUVEC	blood vessel:	n/a	chr9:21802967-21802977
3	YY1	chr9:21802436-21803011	GM12878	blood:	n/a	n/a
4	E2F1	chr9:21802166-21803046	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr9:21801872-21804039	PANC-1	pancreas:	n/a	n/a
6	TBL1XR1	chr9:21802041-21802884	GM12878	blood:	n/a	n/a
7	ZNF217	chr9:21802048-21802699	MCF-7	breast:	n/a	n/a
8	MAX	chr9:21801967-21803842	HepG2	liver:	n/a	chr9:21802967-21802977
9	POLR2A	chr9:21801907-21802880	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr9:21802055-21803938	HepG2	liver:	n/a	n/a
11	SP4	chr9:21802336-21802876	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr9:21802013-21802885	SK-N-SH	brain:	n/a	n/a
13	ARID3A	chr9:21802071-21802841	HepG2	liver:	n/a	n/a
14	POLR2A	chr9:21801886-21803912	SK-N-MC	brain:	n/a	n/a
15	TAF1	chr9:21802465-21803109	HepG2	liver:	n/a	n/a
16	CHD2	chr9:21802051-21803486	GM12878	blood:	n/a	n/a
17	SP1	chr9:21802008-21802863	H1-hESC	embryonic stem cell:	n/a	chr9:21802621-21802630 chr9:21802623-21802636 chr9:21802518-21802525
18	MAX	chr9:21802187-21803760	H1-hESC	embryonic stem cell:	n/a	chr9:21802967-21802977
19	CREB1	chr9:21802451-21803023	A549	lung:	n/a	n/a
20	MXI1	chr9:21802172-21803628	Hela-S3	cervix:	n/a	n/a
21	YY1	chr9:21802403-21802980	A549	lung:	n/a	n/a
22	SMC3	chr9:21801966-21802841	Hela-S3	cervix:	n/a	n/a
23	ELF1	chr9:21801921-21802794	A549	lung:	n/a	n/a
24	TAF1	chr9:21802399-21802818	SK-N-SH	brain:	n/a	n/a
25	FOSL2	chr9:21802183-21802909	A549	lung:	n/a	chr9:21802275-21802289 chr9:21802490-21802504
26	TEAD4	chr9:21802096-21802960	H1-hESC	embryonic stem cell:	n/a	n/a
27	ZBTB33	chr9:21802032-21802816	SK-N-SH	brain:	n/a	chr9:21802249-21802259
28	YY1	chr9:21802451-21803227	GM12878	blood:	n/a	n/a
29	RCOR1	chr9:21801887-21803030	HepG2	liver:	n/a	n/a
30	SIN3AK20	chr9:21802359-21802860	SK-N-SH	brain:	n/a	n/a
31	NFYB	chr9:21802339-21802799	Hela-S3	cervix:	n/a	n/a
32	ZBTB7A	chr9:21802385-21802667	HepG2	liver:	n/a	chr9:21802519-21802526
33	MXI1	chr9:21802117-21803802	GM12878	blood:	n/a	n/a
34	RELA	chr9:21802380-21803410	GM18951	blood:	n/a	n/a
35	POLR2A	chr9:21802361-21803440	GM12892	blood:	n/a	n/a
36	ZBTB33	chr9:21801994-21802732	A549	lung:	n/a	chr9:21802249-21802259
37	REST	chr9:21801964-21803586	A549	lung:	n/a	chr9:21802327-21802340
38	POLR2A	chr9:21802028-21802935	HUVEC	blood vessel:	n/a	n/a
39	GABPA	chr9:21802448-21802833	GM12878	blood:	n/a	n/a
40	POLR2A	chr9:21801981-21803679	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr9:21801950-21803643	PFSK-1	brain:	n/a	n/a
42	HCFC1	chr9:21801475-21804210	Hela-S3	cervix:	n/a	n/a
43	BCLAF1	chr9:21802237-21803665	GM12878	blood:	n/a	chr9:21803052-21803065
44	E2F6	chr9:21802005-21803337	A549	lung:	n/a	chr9:21803191-21803201
45	MAX	chr9:21801861-21803572	ECC-1	luminal epithelium:	n/a	chr9:21802967-21802977
46	POLR2A	chr9:21802469-21803322	A549	lung:	n/a	n/a
47	BCLAF1	chr9:21802276-21803522	GM12878	blood:	n/a	chr9:21803052-21803065
48	MAFK	chr9:21802066-21802601	IMR90	lung:	n/a	n/a
49	ZNF263	chr9:21801422-21803458	HEK293-T-REx	kidney:	n/a	chr9:21801626-21801635 chr9:21802599-21802608
50	POLR2A	chr9:21801752-21803870	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:21334810..21337205-chr9:21800546..21802816,2	MCF-7	breast:
2	chr6:32939770..32940649-chr9:21802247..21802836,2	HCT-116	colon:
3	chr9:21800247..21802715-chr9:22007122..22010872,3	MCF-7	breast:
4	chr22:44319656..44320398-chr9:21801855..21802795,2	Hela-S3	cervix:
5	chr9:21802179..21803949-chr9:21994356..21995893,2	MCF-7	breast:
6	chr9:21801607..21803714-chr9:21992951..21995865,2	MCF-7	breast:

Variant related genes	Relation type
MTAP	TF binding region
ENSG00000264545	TF binding region
ENSG00000198642	Chromatin interaction
ENSG00000240498	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000266446	Chromatin interaction
ENSG00000147883	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000100344	Chromatin interaction
ENSG00000147889	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1335505	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1372057	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1372058	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs1372059	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs1414242	0.83[ASW][hapmap];0.81[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs1414244	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1542075	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1542076	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17833407	0.83[CHB][hapmap]
rs1889680	0.81[JPT][hapmap]
rs2123338	0.81[JPT][hapmap]
rs2891159	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap]
rs3927737	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs3928894	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs4352937	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs4364717	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs4548267	0.89[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs4636294	0.83[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs6475585	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7023474	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs7027989	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7033503	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs869329	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs869330	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs871024	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9298823	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1026981	chr9:21748202-21811697	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
3	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
4	esv2178466	chr9:21802469-21802470	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2165408	MTAP	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21801000-21803400	Active TSS	Stomach Smooth Muscle	stomach
2	chr9:21801400-21803800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr9:21801400-21804200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr9:21801400-21804400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr9:21801400-21804400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:21801400-21804400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:21801600-21803200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:21801600-21803400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:21801600-21803400	Active TSS	Fetal Brain Female	brain
10	chr9:21801600-21803800	Active TSS	Left Ventricle	heart
11	chr9:21801600-21803800	Active TSS	Pancreas	Pancrea
12	chr9:21801600-21804000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr9:21801600-21804000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr9:21801600-21804000	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr9:21801600-21804000	Active TSS	Ovary	ovary
16	chr9:21801600-21804000	Active TSS	Psoas Muscle	Psoas
17	chr9:21801600-21804200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:21801600-21804200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:21801600-21804200	Active TSS	Right Atrium	heart
20	chr9:21801600-21804400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr9:21801600-21804600	Active TSS	HSMMtube	muscle
22	chr9:21801600-21805000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:21801600-21805000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:21801800-21802600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:21801800-21803000	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr9:21801800-21803200	Active TSS	Brain Angular Gyrus	brain
27	chr9:21801800-21803400	Active TSS	Fetal Stomach	stomach
28	chr9:21801800-21803600	Active TSS	Aorta	Aorta
29	chr9:21801800-21803600	Active TSS	Esophagus	oesophagus
30	chr9:21801800-21803600	Active TSS	Lung	lung
31	chr9:21801800-21803800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:21801800-21803800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:21801800-21803800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr9:21801800-21803800	Active TSS	Placenta Amnion	Placenta Amnion
35	chr9:21801800-21804000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr9:21801800-21804000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:21801800-21804000	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr9:21801800-21804000	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr9:21801800-21804000	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr9:21801800-21804000	Active TSS	Right Ventricle	heart
41	chr9:21801800-21804000	Active TSS	Stomach Mucosa	stomach
42	chr9:21801800-21804000	Active TSS	NHDF-Ad	bronchial
43	chr9:21801800-21804200	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr9:21801800-21804200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:21801800-21804200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr9:21801800-21804200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:21801800-21804200	Active TSS	Thymus	Thymus
48	chr9:21801800-21804400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:21801800-21804400	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr9:21801800-21804400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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