Variant report

Variant	rs12237867
Chromosome Location	chr9:26949686-26949687
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	CHD2	chr9:26949582-26950014	Hela-S3	cervix:	n/a	n/a
2	TAF1	chr9:26949505-26949992	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr9:26949452-26950145	Hela-S3	cervix:	n/a	chr9:26949916-26949927
4	POLR2A	chr9:26949381-26950004	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr9:26949461-26950005	HCT-116	colon:	n/a	n/a
6	POLR2A	chr9:26949373-26950029	MCF10A-Er-Src	breast:	n/a	n/a
7	RCOR1	chr9:26949517-26950165	Hela-S3	cervix:	n/a	n/a
8	STAT3	chr9:26949521-26949986	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr9:26949474-26950009	Hela-S3	cervix:	n/a	n/a
10	MAFK	chr9:26949575-26950016	Hela-S3	cervix:	n/a	n/a
11	GATA3	chr9:26949604-26950107	MCF-7	breast:	n/a	n/a
12	MYC	chr9:26949408-26950009	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr9:26949435-26950008	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr9:26949471-26949923	Hela-S3	cervix:	n/a	n/a
15	NFYA	chr9:26949491-26949955	Hela-S3	cervix:	n/a	n/a
16	EP300	chr9:26949491-26950077	Hela-S3	cervix:	n/a	n/a
17	FOS	chr9:26949438-26950095	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr9:26949628-26950083	Hela-S3	cervix:	n/a	n/a
19	STAT3	chr9:26949457-26949968	MCF10A-Er-Src	breast:	n/a	n/a
20	NFYB	chr9:26949508-26949943	Hela-S3	cervix:	n/a	chr9:26949762-26949777
21	POLR2A	chr9:26949673-26949796	K562	blood:	n/a	n/a
22	TFAP2C	chr9:26949623-26950194	Hela-S3	cervix:	n/a	n/a
23	FOSL1	chr9:26949448-26950131	HCT-116	colon:	n/a	n/a
24	KAP1	chr9:26949054-26950050	HEK293	kidney:	n/a	n/a
25	E2F4	chr9:26949184-26949919	MCF10A-Er-Src	breast:	n/a	n/a
26	TBP	chr9:26949400-26950049	Hela-S3	cervix:	n/a	n/a
27	GATA3	chr9:26949594-26950123	SK-N-SH	brain:	n/a	n/a
28	CEBPB	chr9:26949522-26950114	HCT-116	colon:	n/a	chr9:26949916-26949927
29	FOS	chr9:26949517-26950046	MCF10A-Er-Src	breast:	n/a	n/a
30	NR2F2	chr9:26949627-26950104	MCF-7	breast:	n/a	n/a
31	CEBPB	chr9:26949672-26950054	IMR90	lung:	n/a	chr9:26949916-26949927
32	USF2	chr9:26949509-26949871	Hela-S3	cervix:	n/a	n/a
33	BRCA1	chr9:26949520-26950094	Hela-S3	cervix:	n/a	n/a
34	STAT3	chr9:26949591-26950081	Hela-S3	cervix:	n/a	n/a
35	MAX	chr9:26949609-26950195	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr9:26949531-26949832	HCT-116	colon:	n/a	n/a
37	JUND	chr9:26949612-26950027	Hela-S3	cervix:	n/a	n/a
38	FOS	chr9:26949478-26950011	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr9:26949401-26949915	U87	brain:	n/a	n/a
40	SETDB1	chr9:26949038-26950063	U2OS	brain:	n/a	n/a
41	JUN	chr9:26949606-26949988	Hela-S3	cervix:	n/a	n/a
42	CEBPB	chr9:26949413-26950144	HCT-116	colon:	n/a	chr9:26949916-26949927
43	KAP1	chr9:26949524-26950022	U2OS	brain:	n/a	n/a
44	STAT3	chr9:26949514-26949997	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr9:26949458-26950072	Hela-S3	cervix:	n/a	n/a
46	MAX	chr9:26949553-26950099	Hela-S3	cervix:	n/a	n/a
47	RFX5	chr9:26949490-26949994	Hela-S3	cervix:	n/a	n/a
48	RAD21	chr9:26949600-26949995	Hela-S3	cervix:	n/a	n/a
49	TCF7L2	chr9:26949581-26950090	Hela-S3	cervix:	n/a	n/a
50	CCNT2	chr9:26949479-26949959	K562	blood:	n/a	n/a

Variant related genes	Relation type
PLAA	TF binding region

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10511796	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10511798	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10757636	0.81[ASN][1000 genomes]
rs10812490	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10812491	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10812494	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10812495	0.87[AMR][1000 genomes]
rs10812502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10812503	0.84[ASN][1000 genomes]
rs10812504	0.84[ASN][1000 genomes]
rs10812505	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10812506	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10812509	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10812510	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10812513	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10812514	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10812517	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10812522	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10812524	0.88[EUR][1000 genomes]
rs10967581	0.87[AMR][1000 genomes]
rs10967586	0.81[ASN][1000 genomes]
rs10967597	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10967599	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10967602	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967609	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967611	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10967612	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10967614	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10967621	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10967622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10967623	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10967627	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10967629	0.87[ASN][1000 genomes]
rs10967630	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10967632	0.87[ASN][1000 genomes]
rs10967633	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10967635	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10967636	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10967646	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10967649	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10967650	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10967651	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10967661	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967662	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967666	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967668	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967669	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967672	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967673	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10967678	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967681	0.94[EUR][1000 genomes]
rs10967682	0.89[EUR][1000 genomes]
rs10967688	0.94[EUR][1000 genomes]
rs10967694	0.91[EUR][1000 genomes]
rs10967695	0.91[EUR][1000 genomes]
rs10967699	0.88[EUR][1000 genomes]
rs10967701	0.88[EUR][1000 genomes]
rs11534184	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11534185	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11555693	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11562224	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12235490	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12236404	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12236850	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12684983	0.88[EUR][1000 genomes]
rs1336337	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1541144	0.84[ASN][1000 genomes]
rs17760820	0.82[AMR][1000 genomes]
rs17833941	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2184438	0.86[ASN][1000 genomes]
rs2184439	0.84[ASN][1000 genomes]
rs3737226	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3739544	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3739547	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3739548	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3739550	0.83[ASN][1000 genomes]
rs3758218	0.84[ASN][1000 genomes]
rs55827505	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55860736	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55870543	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56307252	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56903929	0.88[EUR][1000 genomes]
rs57450012	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57692080	0.88[EUR][1000 genomes]
rs60281060	0.91[EUR][1000 genomes]
rs60841248	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7019034	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7019075	0.85[AMR][1000 genomes]
rs7020010	0.87[ASN][1000 genomes]
rs7024327	0.91[EUR][1000 genomes]
rs7031903	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7031984	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7034115	0.80[ASN][1000 genomes]
rs7034478	0.84[ASN][1000 genomes]
rs7034888	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7034899	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7035447	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7045339	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72703105	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72719536	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72719538	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7849248	0.85[ASN][1000 genomes]
rs7857447	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7857466	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7857990	0.87[AMR][1000 genomes]
rs7865952	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7869798	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7870787	0.86[ASN][1000 genomes]
rs7872666	0.83[AMR][1000 genomes]
rs7873073	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7874940	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7875068	0.84[ASN][1000 genomes]
rs7875171	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9644870	0.83[AMR][1000 genomes];0.97[EUR][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	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26947600-26955200	Weak transcription	Spleen	Spleen
2	chr9:26948000-26949800	Weak transcription	Placenta	Placenta
3	chr9:26948000-26955200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr9:26948200-26953600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr9:26948200-26953600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr9:26948200-26954000	Weak transcription	Osteobl	bone
7	chr9:26948200-26955000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:26948200-26955000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:26948200-26955000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:26948200-26955000	Weak transcription	Adipose Nuclei	Adipose
11	chr9:26948200-26955000	Weak transcription	Brain Angular Gyrus	brain
12	chr9:26948200-26955000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:26948200-26955000	Weak transcription	Brain Substantia Nigra	brain
14	chr9:26948200-26955000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:26948200-26955000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:26948200-26955000	Weak transcription	NHDF-Ad	bronchial
17	chr9:26948200-26955000	Weak transcription	NHLF	lung
18	chr9:26948200-26955200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:26948200-26955200	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:26948200-26955400	Weak transcription	Psoas Muscle	Psoas
21	chr9:26948200-26955800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:26948400-26950000	Enhancers	HepG2	liver
23	chr9:26948400-26953800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:26948400-26954000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:26948400-26954200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr9:26948400-26954600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:26948400-26955000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:26948400-26955200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr9:26948400-26955200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr9:26948400-26955200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:26948400-26955200	Weak transcription	Liver	Liver
32	chr9:26948800-26950000	Enhancers	HMEC	breast
33	chr9:26949000-26950000	Enhancers	NHEK	skin
34	chr9:26949200-26950600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:26949400-26949800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr9:26949400-26949800	Enhancers	A549	lung
37	chr9:26949400-26949800	Flanking Active TSS	K562	blood
38	chr9:26949400-26949800	Enhancers	NH-A	brain
39	chr9:26949400-26950000	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr9:26949400-26950000	Flanking Active TSS	Hela-S3	cervix
41	chr9:26949600-26950000	Enhancers	Small Intestine	intestine

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