Variant report

Variant	rs929596
Chromosome Location	chr2:234674476-234674477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10178992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10929302	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11673726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11695484	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11888459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11891311	0.95[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12987866	0.88[EUR][1000 genomes]
rs13009407	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13401281	0.85[ASN][1000 genomes]
rs13410335	0.85[ASN][1000 genomes]
rs17862873	0.83[EUR][1000 genomes]
rs17862875	0.85[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17863787	0.81[CEU][hapmap]
rs17864701	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1875263	0.86[JPT][hapmap]
rs1983023	0.88[ASN][1000 genomes]
rs2018985	0.91[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2070959	0.81[CEU][hapmap]
rs2602376	0.84[CEU][hapmap]
rs2741044	0.89[CEU][hapmap]
rs2741045	0.84[CEU][hapmap]
rs2741046	0.84[CEU][hapmap]
rs2885296	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34352510	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3771341	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148324	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148325	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4477910	0.88[ASN][1000 genomes]
rs6431625	0.83[ASN][1000 genomes]
rs6714634	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6722076	0.85[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6742078	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6744284	0.90[CEU][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs6747843	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7564935	0.94[ASW][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7567468	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7604115	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs869283	0.86[JPT][hapmap]
rs887829	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv1811811	chr2:234633964-234709430	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs929596	NPPC	cis	parietal	SCAN
rs929596	EFHD1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234669200-234683800	Weak transcription	Gastric	stomach
2	chr2:234671400-234675200	Enhancers	Fetal Intestine Small	intestine
3	chr2:234672000-234675200	Enhancers	Fetal Intestine Large	intestine
4	chr2:234672800-234685400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:234673200-234674600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:234673600-234674800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:234673600-234676400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:234673800-234674800	Weak transcription	Stomach Mucosa	stomach
9	chr2:234673800-234675000	Weak transcription	A549	lung
10	chr2:234673800-234675400	Enhancers	Duodenum Mucosa	Duodenum
11	chr2:234673800-234676200	Weak transcription	Liver	Liver
12	chr2:234673800-234676400	Weak transcription	NHEK	skin
13	chr2:234673800-234681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:234673800-234683800	Weak transcription	Colonic Mucosa	Colon

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