Variant report

Variant	rs59010837
Chromosome Location	chr4:57301736-57301737
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	MXI1	chr4:57300894-57303518	HepG2	liver:	n/a	n/a
2	TAF1	chr4:57301217-57302795	GM12878	blood:	n/a	n/a
3	MXI1	chr4:57300786-57304245	IMR90	lung:	n/a	n/a
4	MAX	chr4:57301122-57302830	H1-hESC	embryonic stem cell:	n/a	chr4:57302554-57302564 chr4:57301487-57301497 chr4:57302555-57302564 chr4:57301655-57301666 chr4:57301657-57301664 chr4:57302623-57302632 chr4:57302554-57302565 chr4:57301656-57301665 chr4:57301655-57301665 chr4:57302555-57302564 chr4:57302556-57302563 chr4:57301957-57301964
5	TFAP2C	chr4:57301043-57302979	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr4:57301694-57301889	H1-hESC	embryonic stem cell:	n/a	n/a
7	CEBPB	chr4:57301088-57302943	Hela-S3	cervix:	n/a	chr4:57302760-57302771 chr4:57302758-57302771 chr4:57302758-57302769 chr4:57302760-57302771 chr4:57302755-57302772
8	POLR2A	chr4:57300776-57302830	PBDE	blood:	n/a	n/a
9	SIN3AK20	chr4:57300888-57302916	K562	blood:	n/a	n/a
10	HEY1	chr4:57301356-57302785	K562	blood:	n/a	chr4:57301852-57301867
11	RCOR1	chr4:57300494-57302764	K562	blood:	n/a	n/a
12	SIN3AK20	chr4:57301378-57302148	A549	lung:	n/a	n/a
13	FOXM1	chr4:57301351-57302686	GM12878	blood:	n/a	n/a
14	CTCF	chr4:57301680-57301830	GM12874	blood:	n/a	n/a
15	PML	chr4:57300757-57303712	GM12878	blood:	n/a	n/a
16	CTCF	chr4:57301660-57301810	HMEC	breast:	n/a	n/a
17	POLR2A	chr4:57301134-57302723	MCF-7	breast:	n/a	n/a
18	JUND	chr4:57301694-57301893	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr4:57300894-57303737	IMR90	lung:	n/a	n/a
20	BRCA1	chr4:57301534-57302631	HepG2	liver:	n/a	n/a
21	SP1	chr4:57301496-57302566	HepG2	liver:	n/a	chr4:57301883-57301895 chr4:57301884-57301894 chr4:57301884-57301893 chr4:57301883-57301895 chr4:57301885-57301894 chr4:57302163-57302172 chr4:57301885-57301894 chr4:57302161-57302173 chr4:57302161-57302173 chr4:57301880-57301894 chr4:57301827-57301841
22	EP300	chr4:57301508-57302746	K562	blood:	n/a	chr4:57301874-57301890 chr4:57302583-57302599
23	POLR2A	chr4:57301458-57302847	HUVEC	blood vessel:	n/a	n/a
24	ZNF143	chr4:57301048-57302731	GM12878	blood:	n/a	n/a
25	TAF1	chr4:57301604-57301850	GM12878	blood:	n/a	n/a
26	GATA1	chr4:57301610-57302746	PBDE	blood:	n/a	n/a
27	TAF7	chr4:57301454-57302739	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIN3AK20	chr4:57301362-57302279	PFSK-1	brain:	n/a	n/a
29	ATF2	chr4:57301351-57302717	GM12878	blood:	n/a	n/a
30	ZBTB7A	chr4:57301673-57302677	K562	blood:	n/a	n/a
31	SIN3AK20	chr4:57301294-57302225	HepG2	liver:	n/a	n/a
32	HDAC2	chr4:57301668-57302712	MCF-7	breast:	n/a	chr4:57302613-57302622 chr4:57301736-57301745
33	POLR2A	chr4:57301451-57302748	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr4:57301056-57303891	U87	brain:	n/a	n/a
35	ZBTB33	chr4:57301522-57301901	GM12878	blood:	n/a	n/a
36	POLR2A	chr4:57301488-57302714	HepG2	liver:	n/a	n/a
37	USF1	chr4:57301460-57301974	SK-N-SH_RA	brain:	n/a	n/a
38	ELF1	chr4:57301648-57302457	HepG2	liver:	n/a	n/a
39	YY1	chr4:57300980-57302801	GM12878	blood:	n/a	chr4:57301486-57301495 chr4:57301860-57301869 chr4:57301263-57301272
40	POLR2A	chr4:57301084-57304042	HepG2	liver:	n/a	n/a
41	PML	chr4:57301481-57301841	GM12878	blood:	n/a	n/a
42	TCF12	chr4:57300977-57302974	A549	lung:	n/a	n/a
43	MXI1	chr4:57300482-57302815	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr4:57301424-57302804	GM12891	blood:	n/a	n/a
45	TAF1	chr4:57301618-57301896	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr4:57301231-57302767	A549	lung:	n/a	n/a
47	POLR2A	chr4:57300909-57302793	Hela-S3	cervix:	n/a	n/a
48	ZNF143	chr4:57301502-57302565	H1-hESC	embryonic stem cell:	n/a	n/a
49	UBTF	chr4:57299970-57302790	K562	blood:	n/a	n/a
50	YY1	chr4:57301016-57302781	HepG2	liver:	n/a	chr4:57301486-57301495 chr4:57301860-57301869 chr4:57301263-57301272

No.	Distal block	Cell Line	Cell type
1	chr4:57252573..57255971-chr4:57298663..57303783,6	MCF-7	breast:
2	chr4:56411581..56413941-chr4:57300856..57302618,2	K562	blood:
3	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
4	chr4:57298757..57303397-chr4:57395270..57398462,7	K562	blood:
5	chr4:57250870..57256080-chr4:57298204..57304153,16	K562	blood:
6	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
7	chr4:57300392..57305074-chr4:57333261..57337861,17	MCF-7	breast:
8	chr3:87101885..87102401-chr4:57301313..57302001,2	NB4	blood:
9	chr4:57275040..57277242-chr4:57300118..57301937,2	MCF-7	breast:
10	chr4:57299474..57303800-chr4:57395386..57399526,7	K562	blood:
11	chr4:57300865..57304829-chr4:57331110..57333239,4	MCF-7	breast:
12	chr4:57301138..57303431-chr4:57844871..57846919,2	MCF-7	breast:
13	chr4:57299951..57301849-chr4:57773604..57776000,3	K562	blood:
14	chr4:56813951..56816639-chr4:57299941..57302593,2	K562	blood:
15	chr4:57250870..57256510-chr4:57298204..57303491,14	K562	blood:
16	chr4:57251780..57255283-chr4:57300557..57304376,5	MCF-7	breast:
17	chr4:57301355..57303854-chr4:57773620..57776020,4	MCF-7	breast:
18	chr4:57265142..57270324-chr4:57301712..57304176,5	K562	blood:
19	chr14:24583219..24583748-chr4:57301109..57301819,2	NB4	blood:

Variant related genes	Relation type
PPAT	TF binding region
PAICS	TF binding region
ENSG00000084093	Chromatin interaction
ENSG00000249693	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000272969	Chromatin interaction
ENSG00000270109	Chromatin interaction
ENSG00000084092	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000100897	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000174799	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000241293	Chromatin interaction
ENSG00000268171	Chromatin interaction
ENSG00000134852	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17086860	0.86[AFR][1000 genomes]
rs2001807	0.93[AFR][1000 genomes]
rs4073690	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60112184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6818446	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57295000-57305000	Active TSS	GM12878-XiMat	blood
2	chr4:57298400-57305600	Active TSS	Hela-S3	cervix
3	chr4:57299200-57302600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:57299200-57304000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:57299200-57304200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr4:57299200-57304400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:57299200-57304400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr4:57299200-57304800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr4:57299200-57305000	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr4:57299200-57305800	Active TSS	H1 Cell Line	embryonic stem cell
11	chr4:57299200-57305800	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr4:57299200-57305800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr4:57299400-57304200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr4:57299400-57304200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:57299400-57304400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:57299400-57304800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:57299400-57305000	Active TSS	K562	blood
18	chr4:57299600-57304400	Active TSS	A549	lung
19	chr4:57299800-57303000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr4:57299800-57304400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr4:57299800-57304400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:57299800-57304400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:57299800-57304800	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr4:57299800-57305600	Active TSS	HepG2	liver
25	chr4:57300000-57304000	Active TSS	HSMM	muscle
26	chr4:57300000-57304400	Active TSS	Ovary	ovary
27	chr4:57300200-57304000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:57300200-57304000	Active TSS	NH-A	brain
29	chr4:57300400-57303400	Active TSS	Thymus	Thymus
30	chr4:57300400-57304000	Active TSS	NHEK	skin
31	chr4:57300400-57304200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:57300400-57304200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:57300400-57304200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:57300400-57304200	Active TSS	Brain Angular Gyrus	brain
35	chr4:57300400-57304200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:57300400-57304200	Active TSS	Fetal Thymus	thymus
37	chr4:57300600-57303600	Active TSS	Colon Smooth Muscle	Colon
38	chr4:57300600-57303600	Active TSS	Fetal Intestine Small	intestine
39	chr4:57300600-57303600	Active TSS	Fetal Muscle Leg	muscle
40	chr4:57300600-57303600	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr4:57300600-57304000	Active TSS	Muscle Satellite Cultured Cells	--
42	chr4:57300600-57304000	Active TSS	Fetal Stomach	stomach
43	chr4:57300600-57304000	Active TSS	Dnd41	blood
44	chr4:57300600-57304000	Active TSS	HMEC	breast
45	chr4:57300600-57304200	Active TSS	NHLF	lung
46	chr4:57300600-57304400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:57300800-57301800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr4:57300800-57302200	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr4:57300800-57303000	Active TSS	Right Atrium	heart
50	chr4:57300800-57303200	Active TSS	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links