Variant report

Variant	rs1876789
Chromosome Location	chr5:42360730-42360731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10050512	0.91[EUR][1000 genomes]
rs10052738	0.87[CEU][hapmap]
rs10054119	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10060873	0.84[EUR][1000 genomes]
rs10064990	0.85[EUR][1000 genomes]
rs10073423	0.91[EUR][1000 genomes]
rs10079521	0.85[EUR][1000 genomes]
rs10461736	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10462034	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11954853	0.86[EUR][1000 genomes]
rs12153093	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12517869	0.83[ASN][1000 genomes]
rs12519296	1.00[JPT][hapmap]
rs12654986	0.88[ASN][1000 genomes]
rs13189999	0.90[EUR][1000 genomes]
rs1354108	0.85[EUR][1000 genomes]
rs1393017	1.00[JPT][hapmap]
rs1393018	1.00[JPT][hapmap]
rs1501518	0.84[EUR][1000 genomes]
rs1501519	0.84[EUR][1000 genomes]
rs1509460	0.85[GIH][hapmap]
rs1827331	0.84[EUR][1000 genomes]
rs1909951	0.85[EUR][1000 genomes]
rs2940927	0.88[GIH][hapmap]
rs34813199	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35005365	0.88[EUR][1000 genomes]
rs35707555	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3885984	0.91[EUR][1000 genomes]
rs4242098	0.91[EUR][1000 genomes]
rs4305644	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4320267	0.94[EUR][1000 genomes]
rs4404722	0.87[EUR][1000 genomes]
rs4457090	0.93[EUR][1000 genomes]
rs4460174	0.87[EUR][1000 genomes]
rs4489104	0.87[EUR][1000 genomes]
rs4533937	0.87[EUR][1000 genomes]
rs4866812	0.81[ASN][1000 genomes]
rs6451605	0.83[EUR][1000 genomes]
rs6861468	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6861819	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6872878	0.91[EUR][1000 genomes]
rs6888449	0.92[EUR][1000 genomes]
rs7715104	0.87[EUR][1000 genomes]
rs7715374	0.94[EUR][1000 genomes]
rs7718368	0.87[EUR][1000 genomes]
rs9292848	0.91[EUR][1000 genomes]
rs949559	0.98[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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv880518	chr5:42231896-42375243	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv881375	chr5:42254097-42442715	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42359800-42361400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr5:42359800-42361600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:42359800-42362000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:42359800-42362200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr5:42360000-42360800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr5:42360000-42360800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:42360000-42361200	Enhancers	Adipose Nuclei	Adipose
8	chr5:42360000-42361400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:42360000-42361800	Enhancers	NHDF-Ad	bronchial
10	chr5:42360000-42362200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:42360000-42362400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:42360000-42362400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr5:42360200-42361000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:42360200-42361400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:42360400-42360800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr5:42360400-42360800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr5:42360400-42360800	Enhancers	Colon Smooth Muscle	Colon
18	chr5:42360400-42362200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:42360600-42360800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr5:42360600-42361000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:42360600-42361000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr5:42360600-42361000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:42360600-42361000	Enhancers	HUVEC	blood vessel
24	chr5:42360600-42361200	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr5:42360600-42361600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:42360600-42362200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:42360600-42362200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links