Variant report

Variant	rs9944280
Chromosome Location	chr15:31506910-31506911
allele	C/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	CTCF	chr15:31506590-31508289	A549	lung:	n/a	chr15:31507788-31507806 chr15:31507791-31507804 chr15:31507793-31507803 chr15:31507827-31507840
2	SMC3	chr15:31506778-31509180	Hela-S3	cervix:	n/a	chr15:31507060-31507070 chr15:31508657-31508667 chr15:31508046-31508056 chr15:31507794-31507804 chr15:31507790-31507804
3	MAX	chr15:31506693-31509050	HepG2	liver:	n/a	n/a
4	CTCF	chr15:31506840-31506990	GM12873	blood:	n/a	n/a
5	POLR2A	chr15:31506705-31509296	GM12892	blood:	n/a	n/a
6	POLR2A	chr15:31506770-31509334	GM12878	blood:	n/a	n/a
7	CTCF	chr15:31506883-31506952	MCF-7	breast:	n/a	n/a
8	PBX3	chr15:31506777-31506969	GM12878	blood:	n/a	n/a
9	CTCF	chr15:31506860-31507010	GM12873	blood:	n/a	n/a
10	BRCA1	chr15:31506870-31506911	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:31506781-31508367	GM12892	blood:	n/a	n/a
12	SMC3	chr15:31506875-31509137	SK-N-SH	brain:	n/a	chr15:31507060-31507070 chr15:31508657-31508667 chr15:31508046-31508056 chr15:31507794-31507804 chr15:31507790-31507804
13	CTCF	chr15:31506887-31507001	K562	blood:	n/a	n/a
14	CTCF	chr15:31506780-31506930	HEEpiC	esophagus:	n/a	n/a
15	CTCF	chr15:31506840-31506990	GM12875	blood:	n/a	n/a
16	POLR2A	chr15:31506745-31509203	GM15510	blood:	n/a	n/a
17	CTCF	chr15:31506900-31507050	HMF	breast:	n/a	n/a
18	CTCF	chr15:31506840-31506990	NHEK	skin:	n/a	n/a
19	MTA3	chr15:31506588-31509494	GM12878	blood:	n/a	n/a
20	CTCF	chr15:31506870-31507014	NHEK	skin:	n/a	n/a
21	CTCF	chr15:31506820-31506970	GM06990	blood:	n/a	n/a
22	BHLHE40	chr15:31506800-31507151	GM12878	blood:	n/a	n/a
23	CTCF	chr15:31506800-31506950	SAEC	small airway:	n/a	n/a
24	MAX	chr15:31506739-31509280	NB4	blood:	n/a	n/a
25	USF2	chr15:31506806-31507417	Hela-S3	cervix:	n/a	chr15:31507241-31507252
26	CTCF	chr15:31506820-31506970	GM12865	blood:	n/a	n/a
27	SMARCB1	chr15:31506827-31509186	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr15:31506646-31508392	GM12892	blood:	n/a	n/a
29	POLR2A	chr15:31506496-31509522	GM18505	blood:	n/a	n/a
30	POLR2A	chr15:31506401-31509581	GM12878	blood:	n/a	n/a
31	CTCF	chr15:31506900-31507050	GM12864	blood:	n/a	n/a
32	POLR2A	chr15:31506608-31509626	GM19099	blood:	n/a	n/a
33	CTCF	chr15:31506831-31507060	GM12892	blood:	n/a	n/a
34	CTCF	chr15:31506860-31507010	GM12875	blood:	n/a	n/a
35	MAX	chr15:31506881-31509237	Hela-S3	cervix:	n/a	n/a
36	ELF1	chr15:31506672-31509094	GM12878	blood:	n/a	chr15:31507337-31507349 chr15:31508221-31508233 chr15:31508806-31508815
37	MAZ	chr15:31506906-31509009	Hela-S3	cervix:	n/a	n/a
38	HCFC1	chr15:31506825-31509438	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr15:31506860-31507010	HPF	lung:	n/a	n/a
40	CTCF	chr15:31506880-31507030	HEK293	kidney:	n/a	n/a
41	CTCF	chr15:31506880-31507030	NHEK	skin:	n/a	n/a
42	BHLHE40	chr15:31506772-31507136	HepG2	liver:	n/a	n/a
43	RAD21	chr15:31506818-31507382	Hela-S3	cervix:	n/a	chr15:31507344-31507356
44	CTCF	chr15:31506869-31507009	GM19239	blood:	n/a	n/a
45	BHLHE40	chr15:31506862-31507075	K562	blood:	n/a	n/a
46	POLR2A	chr15:31506751-31509296	GM18951	blood:	n/a	n/a
47	CTCF	chr15:31506880-31507030	GM12869	blood:	n/a	n/a
48	CTCF	chr15:31506871-31507005	A549	lung:	n/a	n/a
49	CTCF	chr15:31506853-31507049	HepG2	liver:	n/a	n/a
50	CTCF	chr15:31506860-31507010	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000259448	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10438322	0.97[ASN][1000 genomes]
rs12101670	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12437996	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12439686	0.86[ASN][1000 genomes]
rs1370062	0.97[ASN][1000 genomes]
rs1972825	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28451043	0.80[AMR][1000 genomes]
rs28631253	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28669757	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743235	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6493531	0.97[ASN][1000 genomes]
rs7162278	1.00[ASN][1000 genomes]
rs7162751	0.97[ASN][1000 genomes]
rs754611	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
9	nsv903836	chr15:31330280-31512652	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
10	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
12	nsv903839	chr15:31495113-31576677	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
14	esv3389877	chr15:31506685-31509233	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9944280	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs9944280	GOLGA8R	cis	Heart Left Ventricle	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31501800-31507200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:31503800-31507200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:31503800-31507200	Weak transcription	Aorta	Aorta
4	chr15:31504000-31507600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:31504000-31507800	Enhancers	Placenta	Placenta
6	chr15:31504400-31507800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:31505000-31507200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:31505000-31507200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:31505600-31507200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:31505800-31507200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:31506200-31507200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr15:31506400-31507000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr15:31506400-31507000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:31506400-31507200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:31506400-31507200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr15:31506400-31507200	Enhancers	Liver	Liver
17	chr15:31506400-31507400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:31506400-31507400	Enhancers	Primary B cells from cord blood	blood
19	chr15:31506400-31507400	Enhancers	Primary T cells fromperipheralblood	blood
20	chr15:31506400-31507400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr15:31506400-31507400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr15:31506400-31507400	Enhancers	Esophagus	oesophagus
23	chr15:31506400-31507600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:31506400-31507800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr15:31506400-31508000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr15:31506400-31508000	Flanking Active TSS	Fetal Thymus	thymus
27	chr15:31506600-31507000	Enhancers	Primary T cells from cord blood	blood
28	chr15:31506600-31507000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:31506600-31507000	Enhancers	A549	lung
30	chr15:31506600-31507200	Enhancers	Adipose Nuclei	Adipose
31	chr15:31506600-31507200	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr15:31506600-31507200	Enhancers	HMEC	breast
33	chr15:31506600-31507400	Enhancers	Primary B cells from peripheral blood	blood
34	chr15:31506600-31507400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr15:31506600-31507400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:31506600-31507400	Enhancers	Brain Germinal Matrix	brain
37	chr15:31506600-31507400	Enhancers	Colonic Mucosa	Colon
38	chr15:31506600-31507400	Enhancers	Fetal Brain Female	brain
39	chr15:31506600-31507400	Enhancers	Psoas Muscle	Psoas
40	chr15:31506600-31507600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:31506600-31507600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:31506600-31507600	Enhancers	Fetal Intestine Large	intestine
43	chr15:31506600-31507600	Enhancers	Stomach Mucosa	stomach
44	chr15:31506600-31507800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:31506600-31507800	Enhancers	Lung	lung
46	chr15:31506600-31507800	Enhancers	Right Atrium	heart
47	chr15:31506600-31507800	Flanking Active TSS	Thymus	Thymus
48	chr15:31506600-31507800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr15:31506600-31509400	Enhancers	Fetal Heart	heart
50	chr15:31506800-31507000	Enhancers	Rectal Mucosa Donor 29	rectum

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