Variant report

Variant	rs522638
Chromosome Location	chr2:31805675-31805676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10207755	0.92[ASN][1000 genomes]
rs12467911	0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2208532	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2268799	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2300697	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2300698	0.90[ASN][1000 genomes]
rs2300699	0.88[ASN][1000 genomes]
rs2300701	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2754530	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4952197	0.85[GIH][hapmap]
rs499362	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs502139	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs523349	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524345	0.82[ASN][1000 genomes]
rs559555	0.85[ASN][1000 genomes]
rs569320	0.82[EUR][1000 genomes]
rs589427	0.83[EUR][1000 genomes]
rs599300	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs607294	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs608574	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs623419	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs632148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6749019	0.89[ASN][1000 genomes]
rs676033	0.94[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs681482	0.87[EUR][1000 genomes]
rs682895	0.86[EUR][1000 genomes]
rs765138	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs806645	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv456030	chr2:31598823-31820256	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv456041	chr2:31598823-31820256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv581269	chr2:31598823-31820256	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1007179	chr2:31616112-31835410	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1005032	chr2:31616112-31867450	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1013891	chr2:31629179-31854283	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv535612	chr2:31629179-31854283	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1002988	chr2:31767131-31996924	Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs522638	NLRC4	cis	parietal	SCAN
rs522638	SLC30A6	cis	cerebellum	SCAN
rs522638	SLC30A6	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31803800-31806000	Active TSS	Liver	Liver
2	chr2:31804800-31807000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:31805000-31806000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:31805000-31806000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:31805000-31806200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
6	chr2:31805000-31806200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:31805000-31806200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:31805000-31806400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:31805000-31806400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:31805000-31806800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:31805200-31806000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr2:31805200-31806000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:31805200-31806200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr2:31805200-31806200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr2:31805200-31806200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:31805200-31806400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr2:31805200-31806400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr2:31805200-31806400	Bivalent Enhancer	Esophagus	oesophagus
19	chr2:31805200-31806600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:31805400-31806000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
21	chr2:31805400-31806000	Bivalent Enhancer	Placenta	Placenta
22	chr2:31805400-31806000	Bivalent/Poised TSS	A549	lung
23	chr2:31805400-31806000	Flanking Bivalent TSS/Enh	HMEC	breast
24	chr2:31805400-31806200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr2:31805400-31806200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:31805400-31806200	Enhancers	Gastric	stomach
27	chr2:31805600-31805800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:31805600-31805800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:31805600-31805800	Bivalent/Poised TSS	Fetal Heart	heart
30	chr2:31805600-31805800	Bivalent Enhancer	Lung	lung
31	chr2:31805600-31805800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
32	chr2:31805600-31805800	Bivalent/Poised TSS	NHEK	skin
33	chr2:31805600-31806000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:31805600-31806000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:31805600-31806000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:31805600-31806000	Bivalent/Poised TSS	Fetal Brain Female	brain
37	chr2:31805600-31806200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
38	chr2:31805600-31806200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:31805600-31806200	Bivalent Enhancer	Adipose Nuclei	Adipose
40	chr2:31805600-31806200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr2:31805600-31806400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:31805600-31806800	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links