Variant report

Variant	rs62258642
Chromosome Location	chr3:86843336-86843337
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17023665	1.00[AFR][1000 genomes]
rs17027991	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257265	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62257266	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62258571	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62258572	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62258637	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62258639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62258643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62258644	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62258657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62258659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62259360	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62259363	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62264086	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62264087	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877116	chr3:86518318-86964922	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv877117	chr3:86665408-86927574	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv877118	chr3:86722823-86927574	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv877119	chr3:86722823-86952516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv877120	chr3:86722823-86961118	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv877121	chr3:86732817-86916882	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv877122	chr3:86732817-86927574	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv877123	chr3:86732817-86952516	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv877125	chr3:86794501-86916882	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv877126	chr3:86794501-86927574	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv519148	chr3:86831077-86995124	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv877127	chr3:86832039-86952516	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv1008177	chr3:86841615-86905761	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:86836600-86864400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:86841400-86843400	Enhancers	HSMM	muscle
3	chr3:86841600-86843400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:86841600-86843400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:86841600-86843400	Enhancers	NH-A	brain
6	chr3:86841600-86843400	Enhancers	NHDF-Ad	bronchial
7	chr3:86841600-86843400	Enhancers	NHLF	lung
8	chr3:86841600-86843400	Enhancers	Osteobl	bone
9	chr3:86842400-86843600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:86842400-86844000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:86842400-86844000	Enhancers	Hela-S3	cervix
12	chr3:86842400-86844200	Enhancers	Brain Substantia Nigra	brain
13	chr3:86842600-86843400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:86842600-86843400	Enhancers	Colon Smooth Muscle	Colon
15	chr3:86842600-86843600	Enhancers	Fetal Lung	lung
16	chr3:86842600-86843600	Enhancers	NHEK	skin
17	chr3:86842600-86843800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:86842600-86843800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:86842600-86843800	Enhancers	HMEC	breast
20	chr3:86842600-86844000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:86842600-86844000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr3:86842600-86844800	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr3:86842800-86843400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr3:86842800-86843400	Flanking Active TSS	A549	lung
25	chr3:86842800-86843600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:86842800-86843600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr3:86842800-86843600	Enhancers	Adipose Nuclei	Adipose
28	chr3:86842800-86843600	Enhancers	Fetal Muscle Leg	muscle
29	chr3:86842800-86843600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr3:86842800-86843800	Enhancers	H9 Cell Line	embryonic stem cell
31	chr3:86842800-86843800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:86842800-86843800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr3:86842800-86843800	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr3:86842800-86844000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:86842800-86844000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr3:86842800-86844000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:86842800-86844400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:86843000-86843400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:86843000-86843400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr3:86843000-86843400	Enhancers	Stomach Smooth Muscle	stomach
41	chr3:86843000-86843600	Weak transcription	Aorta	Aorta
42	chr3:86843000-86843600	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr3:86843000-86843800	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr3:86843000-86844000	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr3:86843000-86844000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:86843200-86843400	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:86843200-86843400	Flanking Active TSS	HSMMtube	muscle
48	chr3:86843200-86843600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:86843200-86843600	Enhancers	Brain Hippocampus Middle	brain
50	chr3:86843200-86843600	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links