Variant report

Variant	rs10738601
Chromosome Location	chr9:21801776-21801777
allele	A/T
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	HCFC1	chr9:21801475-21804210	Hela-S3	cervix:	n/a	n/a
2	ZNF263	chr9:21801422-21803458	HEK293-T-REx	kidney:	n/a	chr9:21801626-21801635 chr9:21802599-21802608
3	POLR2A	chr9:21801752-21803870	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:21801614-21803661	HCT-116	colon:	n/a	n/a
5	SIN3A	chr9:21801644-21803997	H1-hESC	embryonic stem cell:	n/a	chr9:21802588-21802601
6	POLR2A	chr9:21801744-21803610	Hela-S3	cervix:	n/a	n/a
7	HA-E2F1	chr9:21801764-21803811	MCF-7	breast:	n/a	chr9:21803191-21803201
8	MAX	chr9:21801722-21801956	H1-hESC	embryonic stem cell:	n/a	n/a
9	MXI1	chr9:21801399-21803844	IMR90	lung:	n/a	n/a
10	MAX	chr9:21801654-21803556	MCF-7	breast:	n/a	chr9:21802967-21802977
11	E2F6	chr9:21801579-21803687	H1-hESC	embryonic stem cell:	n/a	chr9:21803191-21803201
12	CEBPB	chr9:21801775-21802753	H1-hESC	embryonic stem cell:	n/a	chr9:21801943-21801956 chr9:21801943-21801954 chr9:21801943-21801956
13	MAZ	chr9:21801474-21804398	IMR90	lung:	n/a	chr9:21802967-21802977
14	TCF12	chr9:21801574-21803613	A549	lung:	n/a	chr9:21802588-21802598 chr9:21803595-21803602 chr9:21801872-21801879
15	POLR2A	chr9:21801771-21803757	Hela-S3	cervix:	n/a	n/a
16	TBP	chr9:21801722-21803712	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr9:21801537-21803840	A549	lung:	n/a	chr9:21802967-21802977
18	CHD1	chr9:21801689-21803984	IMR90	lung:	n/a	n/a
19	POLR2A	chr9:21801667-21803548	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr9:21801032-21804663	HCT-116	colon:	n/a	n/a
21	POLR2A	chr9:21801581-21806164	H1-hESC	embryonic stem cell:	n/a	n/a
22	ATF2	chr9:21801686-21802601	H1-hESC	embryonic stem cell:	n/a	n/a
23	MXI1	chr9:21801681-21805383	SK-N-SH	brain:	n/a	n/a
24	MAX	chr9:21801634-21803778	H1-hESC	embryonic stem cell:	n/a	chr9:21802967-21802977
25	POLR2A	chr9:21801624-21803950	IMR90	lung:	n/a	n/a
26	POLR2A	chr9:21801727-21803638	HepG2	liver:	n/a	n/a
27	CREB1	chr9:21801596-21802347	H1-hESC	embryonic stem cell:	n/a	n/a
28	KAP1	chr9:21801490-21802011	HEK293	kidney:	n/a	n/a
29	CEBPB	chr9:21801757-21802308	IMR90	lung:	n/a	chr9:21801943-21801956 chr9:21801943-21801954 chr9:21801943-21801956

No.	Distal block	Cell Line	Cell type
1	chr9:21334810..21337205-chr9:21800546..21802816,2	MCF-7	breast:
2	chr9:21464451..21467378-chr9:21800569..21802345,2	MCF-7	breast:
3	chr9:21796497..21798731-chr9:21800652..21802433,2	MCF-7	breast:
4	chr9:21800247..21802715-chr9:22007122..22010872,3	MCF-7	breast:
5	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
ENSG00000266446	Chromatin interaction
ENSG00000147883	Chromatin interaction
ENSG00000147889	Chromatin interaction
ENSG00000240498	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10114559	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10119568	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10119693	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10121449	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10121899	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10738598	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10757244	0.86[EUR][1000 genomes]
rs10757257	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10811597	0.83[EUR][1000 genomes]
rs10811598	0.84[EUR][1000 genomes]
rs10811603	0.86[EUR][1000 genomes]
rs10811608	0.86[EUR][1000 genomes]
rs10811623	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10811625	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10811626	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10811629	0.86[ASN][1000 genomes]
rs10965117	0.84[EUR][1000 genomes]
rs10965128	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10965133	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10965134	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10965135	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10965141	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10965143	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10965144	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10965145	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10965153	0.85[ASN][1000 genomes]
rs11523031	0.86[ASN][1000 genomes]
rs12555601	0.86[EUR][1000 genomes]
rs13298275	0.86[EUR][1000 genomes]
rs1335503	0.86[EUR][1000 genomes]
rs1335510	0.87[EUR][1000 genomes]
rs1335511	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1341866	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1345020	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1345023	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1345024	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1414243	0.86[EUR][1000 genomes]
rs1414253	0.87[EUR][1000 genomes]
rs1561650	0.87[EUR][1000 genomes]
rs2165409	0.86[EUR][1000 genomes]
rs3900787	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3922992	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4265275	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4364717	0.82[EUR][1000 genomes]
rs4615669	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4977567	0.85[ASN][1000 genomes]
rs4977733	0.86[ASN][1000 genomes]
rs58377678	0.84[ASN][1000 genomes]
rs7022754	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7023329	0.85[ASN][1000 genomes]
rs7023954	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7029036	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7033879	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7038523	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7049092	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7863090	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7863942	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7868783	0.86[ASN][1000 genomes]
rs958219	0.86[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	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

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21800000-21801800	Enhancers	Placenta	Placenta
2	chr9:21801000-21801800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr9:21801000-21802000	Enhancers	Spleen	Spleen
4	chr9:21801000-21803400	Active TSS	Stomach Smooth Muscle	stomach
5	chr9:21801200-21801800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:21801200-21801800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr9:21801200-21801800	Enhancers	Primary B cells from peripheral blood	blood
8	chr9:21801200-21801800	Flanking Active TSS	NHDF-Ad	bronchial
9	chr9:21801200-21802000	Flanking Active TSS	Colon Smooth Muscle	Colon
10	chr9:21801200-21802000	Flanking Active TSS	HMEC	breast
11	chr9:21801200-21802000	Flanking Active TSS	NHEK	skin
12	chr9:21801400-21801800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr9:21801400-21801800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:21801400-21801800	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr9:21801400-21801800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr9:21801400-21801800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr9:21801400-21801800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:21801400-21801800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:21801400-21801800	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr9:21801400-21801800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
21	chr9:21801400-21802000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:21801400-21802000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr9:21801400-21802000	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr9:21801400-21802000	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr9:21801400-21802000	Flanking Active TSS	Fetal Heart	heart
26	chr9:21801400-21802000	Flanking Active TSS	A549	lung
27	chr9:21801400-21802000	Flanking Active TSS	NHLF	lung
28	chr9:21801400-21802000	Flanking Active TSS	Osteobl	bone
29	chr9:21801400-21802200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr9:21801400-21802200	Flanking Active TSS	Dnd41	blood
31	chr9:21801400-21802200	Flanking Active TSS	NH-A	brain
32	chr9:21801400-21802400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:21801400-21803800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr9:21801400-21804200	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr9:21801400-21804400	Active TSS	H1 Cell Line	embryonic stem cell
36	chr9:21801400-21804400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:21801400-21804400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:21801600-21801800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:21801600-21801800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
40	chr9:21801600-21801800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
41	chr9:21801600-21801800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
42	chr9:21801600-21801800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:21801600-21801800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
44	chr9:21801600-21801800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
45	chr9:21801600-21801800	Enhancers	Primary B cells from cord blood	blood
46	chr9:21801600-21801800	Enhancers	Primary T cells from cord blood	blood
47	chr9:21801600-21801800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
48	chr9:21801600-21801800	Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr9:21801600-21801800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr9:21801600-21801800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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