Variant report

Variant	rs4377498
Chromosome Location	chr3:67474874-67474875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12489223	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489897	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4320072	0.85[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.84[LWK][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4334653	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4455333	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4515060	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856787	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6548542	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7623396	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637465	0.83[EUR][1000 genomes]
rs7645948	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9824745	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9868494	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9880271	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9880590	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67420200-67479400	Weak transcription	Esophagus	oesophagus
2	chr3:67435600-67509800	Weak transcription	Ovary	ovary
3	chr3:67435600-67534200	Weak transcription	Aorta	Aorta
4	chr3:67442800-67478000	Weak transcription	Lung	lung
5	chr3:67449400-67486600	Weak transcription	Fetal Stomach	stomach
6	chr3:67451200-67487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:67454600-67478000	Weak transcription	Fetal Intestine Small	intestine
8	chr3:67463000-67487400	Weak transcription	Pancreas	Pancrea
9	chr3:67463200-67478400	Weak transcription	Psoas Muscle	Psoas
10	chr3:67463200-67484200	Weak transcription	Right Ventricle	heart
11	chr3:67465400-67489600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:67466600-67484400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:67466600-67486200	Weak transcription	Left Ventricle	heart
14	chr3:67466600-67508400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:67469200-67475200	Weak transcription	Spleen	Spleen
16	chr3:67470000-67479600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:67470600-67478000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:67470600-67482200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:67471200-67478600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:67471200-67487600	Weak transcription	A549	lung
21	chr3:67471200-67503800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:67471400-67475400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:67471400-67475400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:67471400-67497600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:67471600-67483400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:67471600-67483800	Weak transcription	Fetal Lung	lung
27	chr3:67471600-67486600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:67471600-67487600	Weak transcription	Fetal Intestine Large	intestine
29	chr3:67471600-67489200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:67471600-67518800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:67471800-67487800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:67472000-67475000	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:67472000-67482400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:67472000-67506200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:67472000-67509800	Weak transcription	HSMM	muscle
36	chr3:67472200-67476200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:67472600-67475600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:67472600-67483800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:67473200-67475000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:67473400-67492200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:67473400-67521000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:67473600-67476200	Strong transcription	Primary T cells from cord blood	blood
43	chr3:67473600-67487400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:67473600-67487400	Weak transcription	Liver	Liver
45	chr3:67473600-67542000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:67474000-67482400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr3:67474200-67482200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr3:67474600-67475400	Strong transcription	Primary B cells from cord blood	blood
49	chr3:67474600-67475600	Enhancers	Fetal Heart	heart
50	chr3:67474800-67475000	Strong transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links