Variant report

Variant	rs58947223
Chromosome Location	chr1:179050854-179050855
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	GABPA	chr1:179050693-179051496	A549	lung:	n/a	chr1:179051125-179051134
2	POLR2A	chr1:179050648-179052242	MCF-7	breast:	n/a	n/a
3	REST	chr1:179050827-179051228	PANC-1	pancreas:	n/a	chr1:179051054-179051068 chr1:179051054-179051074
4	YY1	chr1:179050780-179051596	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr1:179050421-179053208	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:179050569-179051625	U87	brain:	n/a	n/a
7	SIN3AK20	chr1:179050684-179052245	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr1:179050620-179052113	K562	blood:	n/a	n/a
9	MAX	chr1:179050667-179051337	HUVEC	blood vessel:	n/a	chr1:179050699-179050708
10	RCOR1	chr1:179050595-179051510	HepG2	liver:	n/a	n/a
11	TCF12	chr1:179050456-179052398	A549	lung:	n/a	n/a
12	MEF2A	chr1:179050686-179051199	GM12878	blood:	n/a	n/a
13	TEAD4	chr1:179050389-179051453	K562	blood:	n/a	n/a
14	NFIC	chr1:179050470-179051159	GM12878	blood:	n/a	n/a
15	CUX1	chr1:179050491-179051114	K562	blood:	n/a	n/a
16	CEBPB	chr1:179050376-179051220	GM12878	blood:	n/a	n/a
17	REST	chr1:179050757-179051563	A549	lung:	n/a	chr1:179051054-179051068 chr1:179051054-179051074
18	POLR2A	chr1:179050485-179052344	K562	blood:	n/a	n/a
19	MXI1	chr1:179050568-179052638	SK-N-SH	brain:	n/a	chr1:179051135-179051150
20	SMC3	chr1:179050756-179051243	GM12878	blood:	n/a	chr1:179050896-179050903
21	POLR2A	chr1:179049925-179052426	GM12878	blood:	n/a	n/a
22	TAF1	chr1:179050831-179051343	Hela-S3	cervix:	n/a	n/a
23	MAZ	chr1:179050435-179052538	IMR90	lung:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
24	FOSL2	chr1:179050471-179051311	HepG2	liver:	n/a	n/a
25	USF1	chr1:179050700-179051299	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:179050547-179052186	Hela-S3	cervix:	n/a	n/a
27	ELF1	chr1:179050672-179051383	HepG2	liver:	n/a	chr1:179050813-179050824
28	GABPA	chr1:179050849-179051428	SK-N-SH	brain:	n/a	chr1:179051125-179051134
29	CCNT2	chr1:179050773-179051734	K562	blood:	n/a	n/a
30	POLR2A	chr1:179050648-179051510	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr1:179050676-179051430	K562	blood:	n/a	n/a
32	RFX5	chr1:179050751-179051059	K562	blood:	n/a	chr1:179050848-179050861
33	MTA3	chr1:179050015-179052498	GM12878	blood:	n/a	n/a
34	SIN3AK20	chr1:179050408-179052408	MCF-7	breast:	n/a	n/a
35	MAX	chr1:179050662-179051451	Hela-S3	cervix:	n/a	chr1:179050699-179050708
36	RELA	chr1:179050239-179051560	GM18951	blood:	n/a	chr1:179050571-179050580 chr1:179050571-179050580
37	UBTF	chr1:179050649-179052011	K562	blood:	n/a	n/a
38	RUNX3	chr1:179049989-179051669	GM12878	blood:	n/a	n/a
39	RELA	chr1:179050164-179051395	GM10847	blood:	n/a	chr1:179050571-179050580 chr1:179050571-179050580
40	ZNF143	chr1:179050550-179051452	GM12878	blood:	n/a	n/a
41	TBP	chr1:179050649-179051875	K562	blood:	n/a	n/a
42	EP300	chr1:179050544-179051473	GM12878	blood:	n/a	n/a
43	TAF1	chr1:179050547-179051279	GM12892	blood:	n/a	n/a
44	MYC	chr1:179050372-179052402	K562	blood:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
45	MAX	chr1:179050568-179052474	HepG2	liver:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
46	TCF12	chr1:179050812-179051328	GM12878	blood:	n/a	n/a
47	USF1	chr1:179050616-179051430	ECC-1	luminal epithelium:	n/a	n/a
48	STAT3	chr1:179050403-179051103	GM12878	blood:	n/a	chr1:179051001-179051010 chr1:179050674-179050685 chr1:179051000-179051009 chr1:179050999-179051010
49	KAP1	chr1:179050566-179051461	HEK293	kidney:	n/a	n/a
50	TAF1	chr1:179050615-179051463	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179049954..179052769-chr1:179333565..179337813,7	MCF-7	breast:
2	chr1:179050576..179051115-chr11:120195112..120195904,2	HCT-116	colon:
3	chr1:178837797..178839494-chr1:179049948..179052882,2	K562	blood:
4	chr1:178993182..178999783-chr1:179045102..179052535,14	MCF-7	breast:
5	chr1:179048972..179052099-chr1:179331450..179336701,5	MCF-7	breast:
6	chr1:179049424..179053663-chr1:179259743..179264339,5	MCF-7	breast:
7	chr1:179049160..179052033-chr1:179333339..179335895,3	K562	blood:

Variant related genes	Relation type
TOR3A	TF binding region
ENSG00000162779	Chromatin interaction
ENSG00000116199	Chromatin interaction
ENSG00000116194	Chromatin interaction
ENSG00000057252	Chromatin interaction
ENSG00000181264	Chromatin interaction
ENSG00000263633	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10157052	1.00[AMR][1000 genomes]
rs10157487	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10159048	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28913571	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28913879	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55877399	1.00[AMR][1000 genomes]
rs55895054	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56007923	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56265148	1.00[AMR][1000 genomes]
rs56685652	1.00[AMR][1000 genomes]
rs56948577	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57443960	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58082966	1.00[AMR][1000 genomes]
rs58148372	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59835487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60428208	1.00[AMR][1000 genomes]
rs60642070	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61171624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6681864	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74129722	1.00[AMR][1000 genomes]
rs74129730	1.00[AMR][1000 genomes]
rs74129733	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74129741	1.00[AMR][1000 genomes]
rs74131923	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74131925	1.00[AMR][1000 genomes]
rs9650996	1.00[AMR][1000 genomes]
rs9728409	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179049800-179051000	Flanking Active TSS	GM12878-XiMat	blood
2	chr1:179049800-179051200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr1:179050000-179051000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:179050000-179051000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr1:179050000-179051000	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr1:179050000-179051000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:179050000-179051000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr1:179050000-179051000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr1:179050000-179051000	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr1:179050000-179051000	Flanking Active TSS	Hela-S3	cervix
11	chr1:179050200-179051000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:179050200-179051000	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr1:179050200-179051000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr1:179050200-179051000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr1:179050200-179051000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:179050200-179051000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:179050200-179051000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr1:179050200-179051000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:179050200-179051000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr1:179050200-179051000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:179050200-179051000	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr1:179050200-179051000	Flanking Active TSS	K562	blood
23	chr1:179050200-179051000	Flanking Active TSS	NHEK	skin
24	chr1:179050200-179051200	Flanking Active TSS	Dnd41	blood
25	chr1:179050200-179051200	Flanking Active TSS	HMEC	breast
26	chr1:179050200-179052400	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr1:179050200-179052400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr1:179050200-179052600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:179050400-179051000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:179050400-179051000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr1:179050400-179051000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr1:179050400-179051000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr1:179050400-179051000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:179050400-179051000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr1:179050400-179051000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr1:179050400-179051000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr1:179050400-179051000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:179050400-179051000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr1:179050400-179051000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:179050400-179051000	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr1:179050400-179051000	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr1:179050400-179051000	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr1:179050400-179051000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr1:179050400-179051000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr1:179050400-179051000	Flanking Active TSS	Fetal Muscle Trunk	muscle
46	chr1:179050400-179051000	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr1:179050400-179051000	Flanking Active TSS	Fetal Stomach	stomach
48	chr1:179050400-179051000	Flanking Active TSS	A549	lung
49	chr1:179050400-179051000	Flanking Active TSS	HUVEC	blood vessel
50	chr1:179050400-179051000	Flanking Active TSS	Osteobl	bone

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