Variant report

Variant	rs16830870
Chromosome Location	chr2:189804775-189804776
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10737934	0.81[ASN][1000 genomes]
rs10737935	0.81[ASN][1000 genomes]
rs1155803	0.88[ASN][1000 genomes]
rs13004114	0.97[ASN][1000 genomes]
rs13009963	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010226	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010373	0.99[ASN][1000 genomes]
rs13013611	0.98[ASN][1000 genomes]
rs1400230	0.98[ASN][1000 genomes]
rs1516444	0.98[ASN][1000 genomes]
rs1516445	0.98[ASN][1000 genomes]
rs1516456	0.85[ASN][1000 genomes]
rs1543150	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1829137	0.97[ASN][1000 genomes]
rs1850275	0.84[ASN][1000 genomes]
rs1878203	0.97[ASN][1000 genomes]
rs1878205	0.99[ASN][1000 genomes]
rs1914032	0.86[ASN][1000 genomes]
rs1996312	0.98[ASN][1000 genomes]
rs2037188	0.98[ASN][1000 genomes]
rs2056157	0.99[ASN][1000 genomes]
rs2067991	0.88[ASN][1000 genomes]
rs2459409	0.98[ASN][1000 genomes]
rs2708203	0.86[ASN][1000 genomes]
rs4666766	0.99[ASN][1000 genomes]
rs4666767	0.99[ASN][1000 genomes]
rs4667253	0.82[ASN][1000 genomes]
rs6434301	0.99[ASN][1000 genomes]
rs6712676	0.88[ASN][1000 genomes]
rs6734088	0.97[ASN][1000 genomes]
rs7567967	0.97[ASN][1000 genomes]
rs7570793	0.81[ASN][1000 genomes]
rs7575426	0.99[ASN][1000 genomes]
rs7607018	0.97[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	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv834490	chr2:189703550-189840963	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875608	chr2:189753823-189837995	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1008398	chr2:189794993-189831353	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv1845445	chr2:189796272-189823392	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv1849974	chr2:189796272-189837995	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv584056	chr2:189796272-189841052	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv459992	chr2:189796272-189855943	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
9	nsv584057	chr2:189796272-189855943	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv875609	chr2:189796272-189862097	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv875610	chr2:189796272-189904674	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv875611	chr2:189799499-189837212	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv584058	chr2:189799499-189855943	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16830870	GULP1	cis	cerebellum	SCAN
rs16830870	ZC3H15	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189802200-189805000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:189802800-189805000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr2:189803000-189805000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:189803200-189804800	Weak transcription	Adipose Nuclei	Adipose
5	chr2:189803200-189804800	Weak transcription	NHDF-Ad	bronchial
6	chr2:189803200-189805200	Enhancers	Osteobl	bone
7	chr2:189803200-189805600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:189803200-189807200	Weak transcription	Aorta	Aorta
9	chr2:189803400-189804800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:189804400-189805200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:189804600-189804800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links