Variant report

Variant	rs4647044
Chromosome Location	chr5:60239800-60239801
allele	C/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	FOS	chr5:60239517-60239854	HUVEC	blood vessel:	n/a	n/a
2	CEBPB	chr5:60239540-60239884	Hela-S3	cervix:	n/a	chr5:60239733-60239744
3	FOS	chr5:60239503-60239918	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr5:60239558-60239890	IMR90	lung:	n/a	chr5:60239733-60239744
5	STAT3	chr5:60239576-60239836	MCF10A-Er-Src	breast:	n/a	n/a
6	SPI1	chr5:60239492-60239931	HL-60	blood:	n/a	n/a
7	FOS	chr5:60239514-60239873	MCF10A-Er-Src	breast:	n/a	n/a
8	ZMIZ1	chr5:60239792-60239854	K562	blood:	n/a	n/a
9	MYC	chr5:60239482-60239940	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr5:60239541-60239844	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr5:60239556-60240203	HepG2	liver:	n/a	chr5:60239733-60239744
12	EP300	chr5:60239605-60239938	Hela-S3	cervix:	n/a	n/a
13	STAT3	chr5:60239733-60239933	MCF10A-Er-Src	breast:	n/a	n/a
14	CEBPB	chr5:60239553-60239813	A549	lung:	n/a	chr5:60239733-60239744
15	CEBPB	chr5:60239532-60239892	K562	blood:	n/a	chr5:60239733-60239744
16	FOS	chr5:60239570-60239842	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:59995886..59998322-chr5:60239584..60242446,2	MCF-7	breast:
2	chr5:60232184..60235811-chr5:60236501..60239833,3	K562	blood:
3	chr5:60238903..60240533-chr5:60255101..60257245,2	K562	blood:
4	chr5:60238110..60240722-chr5:60956482..60958434,2	MCF-7	breast:

Variant related genes	Relation type
NDUFAF2	TF binding region
ENSG00000035499	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs4647027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4647034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4647038	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4647064	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4647068	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4647081	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4647104	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4647110	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4647115	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4647120	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4647128	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4647147	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4647164	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4647166	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4647170	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs952231	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv881712	chr5:60116613-60266875	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv881713	chr5:60116613-60305125	Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv598305	chr5:60116613-60308836	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv881714	chr5:60116613-60313015	Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv598306	chr5:60129361-60266875	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv598307	chr5:60129361-60308836	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv881716	chr5:60129361-60313015	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv462199	chr5:60129361-60329624	Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv598308	chr5:60129361-60329624	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv462200	chr5:60135985-60266875	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv598309	chr5:60135985-60266875	Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv598310	chr5:60135985-60308836	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv598311	chr5:60136626-60308836	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	nsv520871	chr5:60141245-60320157	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv881717	chr5:60141245-60372582	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
21	nsv598312	chr5:60147754-60313015	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
22	nsv881718	chr5:60147754-60313015	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv881719	chr5:60167888-60241826	Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
24	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
25	nsv1025896	chr5:60190594-60255004	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
26	esv3447747	chr5:60217244-60241866	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
27	nsv933573	chr5:60224875-60309751	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
28	nsv881721	chr5:60232646-60344399	Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:160 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60189400-60240000	Weak transcription	Spleen	Spleen
2	chr5:60189600-60240000	Weak transcription	Pancreas	Pancrea
3	chr5:60193200-60239800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:60213000-60239800	Weak transcription	Colonic Mucosa	Colon
5	chr5:60213400-60239800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:60214400-60240000	Weak transcription	Brain Substantia Nigra	brain
7	chr5:60214800-60240000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr5:60214800-60240200	Weak transcription	Aorta	Aorta
9	chr5:60221600-60239800	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:60223600-60239800	Weak transcription	Brain Anterior Caudate	brain
11	chr5:60223600-60240200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:60224200-60240000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr5:60224200-60240000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:60224400-60239800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:60224400-60239800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:60224400-60240000	Weak transcription	Fetal Thymus	thymus
17	chr5:60224600-60239800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:60225200-60239800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:60225200-60240000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:60228600-60239800	Weak transcription	Psoas Muscle	Psoas
21	chr5:60232000-60239800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr5:60233600-60240000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:60233600-60240000	Weak transcription	Placenta	Placenta
24	chr5:60233600-60240200	Weak transcription	Lung	lung
25	chr5:60233800-60239800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr5:60233800-60239800	Weak transcription	Fetal Kidney	kidney
27	chr5:60233800-60240000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:60233800-60240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:60233800-60240000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:60233800-60240000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:60233800-60240000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:60233800-60240000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:60233800-60240000	Weak transcription	Gastric	stomach
34	chr5:60233800-60240000	Weak transcription	Left Ventricle	heart
35	chr5:60233800-60240000	Weak transcription	Ovary	ovary
36	chr5:60233800-60240000	Weak transcription	Thymus	Thymus
37	chr5:60233800-60240200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:60233800-60240200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:60233800-60240600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:60234600-60239800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:60235400-60240000	Weak transcription	Esophagus	oesophagus
42	chr5:60236400-60240000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr5:60236400-60240000	Weak transcription	Fetal Stomach	stomach
44	chr5:60237000-60239800	Weak transcription	Fetal Brain Female	brain
45	chr5:60237000-60239800	Weak transcription	Fetal Intestine Large	intestine
46	chr5:60237000-60240000	Weak transcription	Fetal Muscle Leg	muscle
47	chr5:60238600-60239800	Enhancers	Primary T cells from cord blood	blood
48	chr5:60238800-60239800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr5:60238800-60239800	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr5:60238800-60239800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links