Variant report

Variant	rs62279990
Chromosome Location	chr3:154819960-154819961
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:154807454..154810340-chr3:154818810..154822797,4	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10513468	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1370031	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17442808	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4273335	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4273336	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56189742	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56208271	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62279988	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62279989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763852	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868930	chr3:154076125-154820242	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1000140	chr3:154336261-154905740	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv534289	chr3:154535584-154987166	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv532663	chr3:154561578-154960353	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:154800200-154824000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:154800400-154820400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:154800400-154826800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:154807600-154823400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:154808200-154827200	Weak transcription	Fetal Intestine Large	intestine
6	chr3:154808800-154825400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:154811800-154821800	Weak transcription	Fetal Lung	lung
8	chr3:154815600-154827400	Weak transcription	Liver	Liver
9	chr3:154815800-154834000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:154818200-154827400	Genic enhancers	Dnd41	blood
11	chr3:154818400-154820800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:154818400-154821000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:154818800-154820800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:154818800-154820800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:154818800-154820800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:154818800-154827000	Weak transcription	Fetal Thymus	thymus
17	chr3:154819000-154820400	Enhancers	HSMM	muscle
18	chr3:154819000-154820600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:154819000-154820800	Enhancers	Adipose Nuclei	Adipose
20	chr3:154819000-154820800	Enhancers	Osteobl	bone
21	chr3:154819200-154820400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:154819200-154820800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:154819400-154820600	Enhancers	NHLF	lung
24	chr3:154819400-154821200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:154819400-154844400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:154819600-154820400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:154819600-154822400	Weak transcription	HSMMtube	muscle
28	chr3:154819600-154822600	Weak transcription	NH-A	brain
29	chr3:154819600-154827000	Weak transcription	Fetal Intestine Small	intestine
30	chr3:154819600-154828400	Weak transcription	Fetal Kidney	kidney
31	chr3:154819800-154820200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:154819800-154820400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:154819800-154820800	Enhancers	NHDF-Ad	bronchial
34	chr3:154819800-154825400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:154819800-154826400	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links