Variant report

Variant	rs74009639
Chromosome Location	chr15:45747469-45747470
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	EBF1	chr15:45746843-45747484	GM12878	blood:	n/a	n/a
2	NFIC	chr15:45746831-45747538	ECC-1	luminal epithelium:	n/a	n/a
3	RUNX3	chr15:45746974-45747522	GM12878	blood:	n/a	n/a
4	EP300	chr15:45746830-45747757	SK-N-SH	brain:	n/a	n/a
5	MAX	chr15:45746960-45747481	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr15:45746732-45747494	ECC-1	luminal epithelium:	n/a	n/a
7	ZNF263	chr15:45747088-45747601	HEK293-T-REx	kidney:	n/a	chr15:45747378-45747387
8	TEAD4	chr15:45746958-45747505	ECC-1	luminal epithelium:	n/a	n/a
9	SMC3	chr15:45746936-45747470	Hela-S3	cervix:	n/a	n/a
10	TCF12	chr15:45746800-45747909	SK-N-SH	brain:	n/a	chr15:45747508-45747518
11	NFIC	chr15:45746811-45747836	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr15:45747002-45747521	U87	brain:	n/a	n/a
13	RXRA	chr15:45746891-45747581	SK-N-SH	brain:	n/a	chr15:45747120-45747140
14	POLR2A	chr15:45746801-45747499	PANC-1	pancreas:	n/a	n/a
15	TCF12	chr15:45746771-45747880	SK-N-SH	brain:	n/a	chr15:45747508-45747518
16	EP300	chr15:45747075-45747558	SK-N-SH_RA	brain:	n/a	n/a
17	PBX3	chr15:45746908-45747560	SK-N-SH	brain:	n/a	n/a
18	STAT3	chr15:45747020-45747532	MCF10A-Er-Src	breast:	n/a	chr15:45747379-45747391 chr15:45747186-45747197
19	RUNX3	chr15:45746943-45747502	GM12878	blood:	n/a	n/a
20	TEAD4	chr15:45746961-45747479	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr15:45746881-45747816	IMR90	lung:	n/a	n/a
22	NFIC	chr15:45746789-45747572	ECC-1	luminal epithelium:	n/a	n/a
23	MAX	chr15:45746870-45747484	A549	lung:	n/a	n/a
24	NFIC	chr15:45746895-45747716	SK-N-SH	brain:	n/a	n/a
25	MYC	chr15:45747044-45747711	NB4	blood:	n/a	n/a
26	STAT3	chr15:45746932-45747556	MCF10A-Er-Src	breast:	n/a	chr15:45747379-45747391 chr15:45747186-45747197
27	PBX3	chr15:45746976-45747496	SK-N-SH	brain:	n/a	n/a
28	TCF12	chr15:45746826-45747510	ECC-1	luminal epithelium:	n/a	n/a
29	STAT3	chr15:45746974-45747532	MCF10A-Er-Src	breast:	n/a	chr15:45747379-45747391 chr15:45747186-45747197
30	MYC	chr15:45746962-45747521	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr15:45747092-45747541	MCF10A-Er-Src	breast:	n/a	n/a
32	GATA3	chr15:45747003-45747544	SK-N-SH	brain:	n/a	n/a
33	EBF1	chr15:45746976-45747605	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:45747039-45747491	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45457588..45459238-chr15:45747257..45749159,2	K562	blood:
2	chr15:45737247..45739664-chr15:45747415..45750054,2	K562	blood:
3	chr15:45745258..45747507-chr15:45747517..45749111,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259354	TF binding region
ENSG00000252285	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs8025019	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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
3	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv442701	chr15:45737096-45748752	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs74009639	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs74009639	GATM	cis	Muscle Skeletal	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45744200-45748400	Weak transcription	Lung	lung
2	chr15:45744800-45748600	Weak transcription	Fetal Intestine Small	intestine
3	chr15:45745200-45749800	Weak transcription	Liver	Liver
4	chr15:45746000-45747600	Enhancers	Gastric	stomach
5	chr15:45746000-45747800	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr15:45746000-45750000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:45746000-45750000	Enhancers	Stomach Mucosa	stomach
8	chr15:45746200-45749800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:45746200-45750000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr15:45746200-45750000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:45746200-45750000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:45746200-45750000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr15:45746200-45750800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr15:45746400-45748600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:45746400-45749800	Enhancers	Primary B cells from cord blood	blood
16	chr15:45746400-45749800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:45746400-45750000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:45746400-45750000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:45746400-45750000	Enhancers	Placenta	Placenta
20	chr15:45746600-45749000	Enhancers	Thymus	Thymus
21	chr15:45746600-45749800	Enhancers	Primary hematopoietic stem cells	blood
22	chr15:45746600-45750000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr15:45746600-45750000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:45746600-45750000	Enhancers	HSMM	muscle
25	chr15:45746800-45747600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr15:45746800-45747600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:45746800-45747600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr15:45746800-45747600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:45746800-45747600	Enhancers	Esophagus	oesophagus
30	chr15:45746800-45747600	Enhancers	Small Intestine	intestine
31	chr15:45746800-45747600	Enhancers	Spleen	Spleen
32	chr15:45746800-45747600	Flanking Active TSS	Dnd41	blood
33	chr15:45746800-45747600	Flanking Bivalent TSS/Enh	HepG2	liver
34	chr15:45746800-45747600	Flanking Active TSS	NH-A	brain
35	chr15:45746800-45747800	Enhancers	Primary T cells from cord blood	blood
36	chr15:45746800-45747800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:45746800-45747800	Enhancers	Adipose Nuclei	Adipose
38	chr15:45746800-45747800	Enhancers	Fetal Thymus	thymus
39	chr15:45746800-45747800	Active TSS	Rectal Smooth Muscle	rectum
40	chr15:45746800-45747800	Flanking Active TSS	A549	lung
41	chr15:45746800-45747800	Flanking Active TSS	GM12878-XiMat	blood
42	chr15:45746800-45747800	Flanking Active TSS	Hela-S3	cervix
43	chr15:45746800-45747800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr15:45746800-45747800	Flanking Active TSS	Osteobl	bone
45	chr15:45746800-45748600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:45746800-45749400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr15:45746800-45750000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:45746800-45750000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:45746800-45750000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:45746800-45750000	Enhancers	NHDF-Ad	bronchial

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