Variant report

Variant	rs10942719
Chromosome Location	chr5:74058398-74058399
allele	G/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	ZBTB33	chr5:74058349-74058927	SK-N-SH	brain:	n/a	n/a
2	MAX	chr5:74058371-74058854	SK-N-SH	brain:	n/a	n/a
3	FOSL2	chr5:74058377-74058748	MCF-7	breast:	n/a	n/a
4	CEBPB	chr5:74058379-74058940	A549	lung:	n/a	n/a
5	FOSL2	chr5:74058240-74059009	SK-N-SH	brain:	n/a	chr5:74058970-74058981
6	POLR2A	chr5:74058386-74058737	HCT-116	colon:	n/a	n/a
7	TEAD4	chr5:74058292-74059027	SK-N-SH	brain:	n/a	n/a
8	SP1	chr5:74058248-74058886	HCT-116	colon:	n/a	n/a
9	ATF3	chr5:74058322-74058905	HCT-116	colon:	n/a	n/a
10	TCF12	chr5:74058186-74059027	SK-N-SH	brain:	n/a	n/a
11	FOSL2	chr5:74058390-74058728	HepG2	liver:	n/a	n/a
12	PBX3	chr5:74058274-74058960	SK-N-SH	brain:	n/a	n/a
13	GATA3	chr5:74058187-74058992	A549	lung:	n/a	n/a
14	CEBPB	chr5:74058361-74058848	Hela-S3	cervix:	n/a	n/a
15	FOS	chr5:74058385-74058902	MCF10A-Er-Src	breast:	n/a	chr5:74058562-74058573
16	JUN	chr5:74058391-74058851	Hela-S3	cervix:	n/a	n/a
17	JUND	chr5:74058362-74058828	Hela-S3	cervix:	n/a	chr5:74058612-74058623 chr5:74058562-74058573
18	POLR2A	chr5:74058312-74058868	SK-N-SH	brain:	n/a	n/a
19	EP300	chr5:74058381-74058862	Hela-S3	cervix:	n/a	n/a
20	FOSL2	chr5:74058282-74058862	SK-N-SH	brain:	n/a	n/a
21	JUND	chr5:74058381-74058727	A549	lung:	n/a	chr5:74058612-74058623 chr5:74058562-74058573
22	EP300	chr5:74058396-74058706	SK-N-SH_RA	brain:	n/a	n/a
23	FOSL2	chr5:74058316-74058853	A549	lung:	n/a	n/a
24	JUND	chr5:74058252-74058851	HCT-116	colon:	n/a	chr5:74058612-74058623 chr5:74058562-74058573
25	ATF3	chr5:74058322-74058912	HCT-116	colon:	n/a	n/a
26	STAT3	chr5:74058394-74058837	MCF10A-Er-Src	breast:	n/a	n/a
27	FOSL2	chr5:74058374-74058780	A549	lung:	n/a	n/a
28	GATA3	chr5:74058217-74058929	SK-N-SH	brain:	n/a	n/a
29	GATA3	chr5:74058229-74059042	SK-N-SH	brain:	n/a	n/a
30	JUND	chr5:74058317-74059083	SK-N-SH	brain:	n/a	chr5:74058612-74058623 chr5:74058562-74058573 chr5:74058970-74058981
31	MYC	chr5:74058365-74058864	MCF10A-Er-Src	breast:	n/a	n/a
32	SP1	chr5:74058335-74058805	A549	lung:	n/a	n/a
33	GATA2	chr5:74058390-74058750	HUVEC	blood vessel:	n/a	n/a
34	EP300	chr5:74058188-74059039	SK-N-SH	brain:	n/a	n/a
35	TCF12	chr5:74058165-74059057	SK-N-SH	brain:	n/a	n/a
36	TCF12	chr5:74058361-74058824	ECC-1	luminal epithelium:	n/a	n/a
37	CEBPB	chr5:74058256-74058963	HCT-116	colon:	n/a	n/a
38	FOS	chr5:74058390-74059712	MCF10A-Er-Src	breast:	n/a	chr5:74059396-74059403 chr5:74058562-74058573 chr5:74059530-74059541 chr5:74059396-74059404 chr5:74058970-74058981
39	SP1	chr5:74058248-74058903	HCT-116	colon:	n/a	n/a
40	RXRA	chr5:74058282-74058894	SK-N-SH	brain:	n/a	n/a
41	SIN3AK20	chr5:74058342-74058770	SK-N-SH	brain:	n/a	n/a
42	FOS	chr5:74058387-74058823	MCF10A-Er-Src	breast:	n/a	chr5:74058562-74058573
43	JUND	chr5:74058297-74058927	HCT-116	colon:	n/a	chr5:74058612-74058623 chr5:74058562-74058573
44	FOSL1	chr5:74058359-74059020	HCT-116	colon:	n/a	chr5:74058970-74058981
45	NFIC	chr5:74058242-74058933	SK-N-SH	brain:	n/a	n/a
46	JUND	chr5:74058218-74058982	SK-N-SH	brain:	n/a	chr5:74058612-74058623 chr5:74058562-74058573 chr5:74058970-74058981
47	CEBPB	chr5:74058275-74058833	HCT-116	colon:	n/a	n/a
48	FOS	chr5:74058385-74058905	MCF10A-Er-Src	breast:	n/a	chr5:74058562-74058573
49	JUND	chr5:74058294-74059041	SK-N-SH	brain:	n/a	chr5:74058612-74058623 chr5:74058562-74058573 chr5:74058970-74058981

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74058294..74061098-chr5:74061736..74064363,2	K562	blood:

Variant related genes	Relation type
NSA2	TF binding region
ENSG00000164346	Chromatin interaction
ENSG00000164347	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12516674	0.89[MKK][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10942719	NSA2	cis	lymphoblastoid	seeQTL
rs10942719	NSA2	cis	cerebellum	SCAN
rs10942719	NSA2	cis	parietal	SCAN
rs10942719	FCHO2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:73999800-74060800	Weak transcription	Pancreas	Pancrea
3	chr5:73999800-74062200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:74002600-74061800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:74008400-74060200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr5:74008400-74060200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:74010400-74059600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:74018000-74060800	Weak transcription	Gastric	stomach
9	chr5:74018600-74062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:74019200-74058600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:74021600-74060800	Weak transcription	Spleen	Spleen
12	chr5:74022000-74060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:74025000-74062000	Weak transcription	Aorta	Aorta
14	chr5:74044400-74061000	Weak transcription	Fetal Heart	heart
15	chr5:74044400-74061000	Weak transcription	Right Ventricle	heart
16	chr5:74045000-74059600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:74045200-74061800	Weak transcription	Esophagus	oesophagus
18	chr5:74045800-74058800	Strong transcription	Primary T cells from cord blood	blood
19	chr5:74047400-74061800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:74050800-74059200	Strong transcription	Fetal Thymus	thymus
21	chr5:74051000-74059600	Strong transcription	Primary B cells from cord blood	blood
22	chr5:74051200-74060000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:74051400-74058400	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:74051400-74059800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr5:74051400-74060200	Strong transcription	Liver	Liver
26	chr5:74051400-74061200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:74051600-74059600	Strong transcription	Placenta	Placenta
28	chr5:74051600-74059600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr5:74051600-74060000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr5:74051800-74058800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:74052000-74058800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr5:74052000-74059000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:74052000-74059200	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr5:74052000-74059600	Strong transcription	Dnd41	blood
35	chr5:74052200-74059400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:74052200-74059400	Strong transcription	Adipose Nuclei	Adipose
37	chr5:74052200-74060400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr5:74052400-74059000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr5:74052400-74059200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr5:74052800-74058400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:74052800-74059400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:74052800-74059600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr5:74052800-74060800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:74052800-74061000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:74052800-74061000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:74052800-74061000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr5:74052800-74061200	Weak transcription	Brain Substantia Nigra	brain
48	chr5:74052800-74062000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:74053000-74059400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:74053600-74060800	Weak transcription	Fetal Stomach	stomach

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