Variant report

Variant	rs2990701
Chromosome Location	chr1:160956745-160956746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1023115	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs12030262	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.84[ASN][1000 genomes]
rs12723902	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12743772	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243479	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246139	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap]
rs2246598	0.80[EUR][1000 genomes]
rs2250288	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2256633	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2481072	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483143	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2483144	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2483148	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28365978	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2988723	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2990700	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2990704	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2990705	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656975	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7530765	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546890	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9427367	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers 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 miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv10894	chr1:160953742-160960609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3509633	chr1:160954381-160957557	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2990701	F11R	cis	parietal	SCAN
rs2990701	USF1	cis	multi-tissue	Pritchard
rs2990701	PMF1	cis	cerebellum	SCAN
rs2990701	CD1A	cis	parietal	SCAN
rs2990701	F11R	cis	lymphoblastoid	seeQTL
rs2990701	APOA2	cis	cerebellum	SCAN
rs2990701	ARHGEF11	cis	cerebellum	SCAN
rs2990701	MNDA	cis	cerebellum	SCAN
rs2990701	OR6N2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160943200-160959800	Weak transcription	Pancreas	Pancrea
2	chr1:160948600-160968000	Weak transcription	Ovary	ovary
3	chr1:160952200-160964400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:160952200-160967000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:160952400-160957200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:160953200-160966600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:160953800-160968200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:160954200-160959800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:160955800-160964400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:160956200-160957000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:160956200-160957200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:160956400-160957600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:160956600-160957000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr1:160956600-160957200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:160956600-160957600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:160956600-160957800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:160956600-160957800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr1:160956600-160958000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr1:160956600-160958600	Enhancers	H1 Cell Line	embryonic stem cell

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