Variant report

Variant	rs396790
Chromosome Location	chr4:79258862-79258863
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs17459809	0.96[EUR][1000 genomes]
rs1840388	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs370252	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs370865	1.00[EUR][1000 genomes]
rs371923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs373144	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs376809	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs381765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs386832	1.00[EUR][1000 genomes]
rs395192	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs397439	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs397449	1.00[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs405190	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs410660	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs417796	0.96[EUR][1000 genomes]
rs420238	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs423884	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs431812	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs438511	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs441064	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs446773	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs454649	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4569782	0.96[EUR][1000 genomes]
rs644235	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs737397	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs931277	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv4399	chr4:79251832-79284571	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv14891	chr4:79256788-79263029	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79221200-79263000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:79230200-79268600	Weak transcription	Pancreas	Pancrea
3	chr4:79231600-79260400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:79238000-79263200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:79240400-79263000	Weak transcription	Psoas Muscle	Psoas
6	chr4:79253800-79264800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:79254600-79261600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:79255800-79259000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:79256400-79259600	Enhancers	Fetal Heart	heart
10	chr4:79256400-79265200	Strong transcription	HepG2	liver
11	chr4:79256600-79261800	Weak transcription	Aorta	Aorta
12	chr4:79257400-79259000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:79257400-79259000	Enhancers	Ovary	ovary
14	chr4:79257400-79259000	Enhancers	HSMMtube	muscle
15	chr4:79257400-79259200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:79257600-79259000	Enhancers	Fetal Muscle Leg	muscle
17	chr4:79257600-79259200	Enhancers	Brain Germinal Matrix	brain
18	chr4:79257800-79259000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:79257800-79259000	Enhancers	NHDF-Ad	bronchial
20	chr4:79257800-79259200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr4:79258000-79259000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
22	chr4:79258000-79261800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:79258000-79275200	Weak transcription	Fetal Brain Female	brain
24	chr4:79258200-79260800	Weak transcription	Right Atrium	heart
25	chr4:79258200-79261800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:79258200-79262000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr4:79258200-79262600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:79258200-79263200	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr4:79258200-79263400	Weak transcription	Fetal Stomach	stomach
30	chr4:79258200-79264400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:79258400-79259000	Genic enhancers	H9 Cell Line	embryonic stem cell
32	chr4:79258400-79259000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:79258400-79259000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr4:79258400-79259800	Weak transcription	Fetal Intestine Large	intestine
35	chr4:79258400-79260800	Strong transcription	Fetal Intestine Small	intestine
36	chr4:79258400-79263000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:79258400-79265800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:79258400-79268600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:79258400-79268600	Weak transcription	Fetal Brain Male	brain
40	chr4:79258400-79269000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr4:79258600-79259000	Enhancers	Placenta	Placenta
42	chr4:79258600-79260600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:79258800-79259000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:79258800-79259000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:79258800-79259000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr4:79258800-79259000	Enhancers	Fetal Muscle Trunk	muscle
47	chr4:79258800-79276800	Weak transcription	Fetal Kidney	kidney
48	chr4:79258800-79291000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links