Variant report

Variant	rs309871
Chromosome Location	chr4:48338582-48338583
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48270541..48273741-chr4:48337743..48341343,4	K562	blood:

Variant related genes	Relation type
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11723080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs309868	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309870	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309887	0.84[AMR][1000 genomes]
rs418214	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695369	0.83[ASN][1000 genomes]
rs55784928	0.81[ASN][1000 genomes]
rs55860639	0.83[ASN][1000 genomes]
rs62309393	0.84[ASN][1000 genomes]
rs62309398	0.86[ASN][1000 genomes]
rs62309399	0.86[ASN][1000 genomes]
rs62309400	0.88[ASN][1000 genomes]
rs62309401	0.88[ASN][1000 genomes]
rs62309402	0.88[ASN][1000 genomes]
rs6833004	1.00[CEU][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48330000-48342400	Weak transcription	Esophagus	oesophagus
2	chr4:48331600-48339400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:48331600-48339600	Weak transcription	Stomach Mucosa	stomach
4	chr4:48331600-48340800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:48332600-48339200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:48333000-48341800	Weak transcription	A549	lung
7	chr4:48333000-48342400	Weak transcription	Left Ventricle	heart
8	chr4:48334000-48341400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:48334200-48339600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:48334200-48340200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:48334200-48342000	Weak transcription	Fetal Heart	heart
12	chr4:48334200-48342000	Weak transcription	HSMM	muscle
13	chr4:48334200-48342200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr4:48334200-48342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:48334400-48342400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:48334800-48341600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:48335600-48339600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:48335800-48342000	Weak transcription	Fetal Kidney	kidney
19	chr4:48336400-48338800	Weak transcription	NHEK	skin
20	chr4:48336400-48339000	Weak transcription	HMEC	breast
21	chr4:48336400-48339400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:48336400-48342000	Weak transcription	Osteobl	bone
23	chr4:48336800-48339200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:48337200-48339800	Weak transcription	Fetal Lung	lung
25	chr4:48337400-48339000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:48337400-48339200	Weak transcription	Thymus	Thymus
27	chr4:48337400-48341600	Weak transcription	HSMMtube	muscle
28	chr4:48337600-48338600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr4:48337600-48339000	Weak transcription	Placenta	Placenta
30	chr4:48337600-48341400	Enhancers	K562	blood
31	chr4:48337600-48341800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr4:48337600-48342400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr4:48337800-48339000	Weak transcription	Fetal Thymus	thymus
34	chr4:48337800-48339800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:48338000-48339000	Enhancers	NHDF-Ad	bronchial
36	chr4:48338200-48340600	Weak transcription	Psoas Muscle	Psoas
37	chr4:48338400-48341000	Weak transcription	NHLF	lung
38	chr4:48338400-48341600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:48338400-48341600	Weak transcription	Hela-S3	cervix
40	chr4:48338400-48342200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:48338400-48342200	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links