Variant report

Variant	rs7538168
Chromosome Location	chr1:185669201-185669202
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10489707	1.00[JPT][hapmap]
rs11579889	0.84[EUR][1000 genomes]
rs11583092	0.84[EUR][1000 genomes]
rs11583867	1.00[CHB][hapmap];0.83[TSI][hapmap]
rs11584252	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587852	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11589543	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807146	0.81[TSI][hapmap]
rs12079064	1.00[CHB][hapmap]
rs12087032	1.00[CHB][hapmap];0.86[TSI][hapmap]
rs1322359	1.00[CHB][hapmap];0.86[TSI][hapmap]
rs1358871	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407430	1.00[CHB][hapmap];0.86[TSI][hapmap]
rs1407431	1.00[CHB][hapmap];0.86[TSI][hapmap]
rs1484134	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484135	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1552281	0.84[EUR][1000 genomes]
rs16824390	0.85[EUR][1000 genomes]
rs16824396	0.84[EUR][1000 genomes]
rs17445778	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs17446906	1.00[CHB][hapmap]
rs17448216	1.00[CHB][hapmap]
rs17448230	1.00[CHB][hapmap]
rs1951517	1.00[CHB][hapmap]
rs2004324	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2057382	0.86[TSI][hapmap]
rs2170859	1.00[CHB][hapmap]
rs2220128	0.81[TSI][hapmap]
rs34923020	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35425624	1.00[CHB][hapmap];0.89[TSI][hapmap]
rs41357745	1.00[CHB][hapmap]
rs41519044	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4651287	0.81[TSI][hapmap]
rs55993167	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56031313	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56238699	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57146145	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58708412	0.94[EUR][1000 genomes]
rs59197925	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59253277	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59702468	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60074235	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60376365	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61829644	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61831462	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61831464	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61831470	0.87[EUR][1000 genomes]
rs61831480	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61831482	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61831483	0.84[EUR][1000 genomes]
rs61831485	0.81[EUR][1000 genomes]
rs61831486	0.84[EUR][1000 genomes]
rs61831502	0.84[EUR][1000 genomes]
rs61831503	0.84[EUR][1000 genomes]
rs61831504	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61831505	0.84[EUR][1000 genomes]
rs61831519	0.86[EUR][1000 genomes]
rs61831521	0.81[EUR][1000 genomes]
rs6656530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668606	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668607	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692602	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727759	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534755	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547022	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554903	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs900775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9286857	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs936723	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9628625	1.00[CHB][hapmap]
rs992760	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs994970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7538168	NMNAT2	cis	parietal	SCAN
rs7538168	PDC	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185664400-185673200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:185665800-185670200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:185668600-185669600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr1:185668600-185670000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
5	chr1:185668600-185670200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
6	chr1:185668800-185669400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:185668800-185669600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:185668800-185669600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:185668800-185669800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
10	chr1:185668800-185670000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
11	chr1:185668800-185670000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
12	chr1:185669000-185670400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr1:185669000-185670800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:185669200-185669400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr1:185669200-185669600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:185669200-185670000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links