Variant report

Variant	rs1374787
Chromosome Location	chr3:160700144-160700145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10154889	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10433352	0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10513560	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs10936215	0.84[EUR][1000 genomes]
rs10936216	0.86[EUR][1000 genomes]
rs11715733	0.80[ASN][1000 genomes]
rs11720263	0.81[MEX][hapmap]
rs12690576	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs13098529	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13256	0.81[MEX][hapmap]
rs1374790	0.84[JPT][hapmap]
rs1374795	0.85[JPT][hapmap]
rs1447608	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1447609	0.86[EUR][1000 genomes]
rs1447622	0.84[JPT][hapmap]
rs1447626	0.95[CEU][hapmap]
rs1530636	0.83[CEU][hapmap];0.83[CHD][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs1562465	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs1580254	0.95[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs16831796	0.97[CHD][hapmap];0.95[JPT][hapmap]
rs1868108	1.00[CEU][hapmap]
rs1868109	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2014810	0.81[ASN][1000 genomes]
rs2121721	0.84[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2376476	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2376477	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2889390	0.86[JPT][hapmap]
rs2889391	0.86[EUR][1000 genomes]
rs34462546	0.85[EUR][1000 genomes]
rs34884182	0.89[EUR][1000 genomes]
rs4521287	0.81[MEX][hapmap]
rs4679928	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441345	0.80[CHD][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs6441346	0.85[EUR][1000 genomes]
rs6763532	0.85[EUR][1000 genomes]
rs6769927	0.86[EUR][1000 genomes]
rs6770180	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6774203	0.83[CEU][hapmap];0.80[CHD][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs6791375	0.89[EUR][1000 genomes]
rs6806015	0.95[ASN][1000 genomes]
rs6808311	0.88[EUR][1000 genomes]
rs6808386	0.84[CEU][hapmap]
rs733948	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs745707	0.84[EUR][1000 genomes]
rs7610432	0.82[ASN][1000 genomes]
rs7611005	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7613316	0.83[CEU][hapmap]
rs7616249	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7624185	0.82[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs7628389	1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7635796	0.84[CEU][hapmap]
rs7640874	0.83[CEU][hapmap]
rs7644586	0.84[CEU][hapmap]
rs898677	1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs956447	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs964533	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9812507	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9813700	0.80[EUR][1000 genomes]
rs9822435	0.86[JPT][hapmap]
rs9832109	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs9839984	0.95[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs9846254	0.84[TSI][hapmap]
rs9857743	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs9857855	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9858335	0.95[CEU][hapmap];0.85[CHD][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs9860182	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs9873705	0.89[EUR][1000 genomes]
rs9881807	1.00[CEU][hapmap]
rs9883566	0.81[JPT][hapmap]

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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1007004	chr3:160695108-160718154	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1374787	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs1374787	C3orf57	cis	parietal	SCAN
rs1374787	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160670400-160700400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:160695200-160701400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:160696200-160700600	Enhancers	Dnd41	blood
4	chr3:160697000-160704000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:160697200-160710600	Weak transcription	Left Ventricle	heart
6	chr3:160697800-160701400	Enhancers	Primary hematopoietic stem cells	blood
7	chr3:160698200-160700800	Enhancers	Primary B cells from peripheral blood	blood
8	chr3:160698200-160700800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:160698200-160701000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:160699200-160701200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr3:160699200-160701600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:160699400-160700600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:160699800-160700200	Enhancers	Placenta	Placenta
14	chr3:160699800-160701200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr3:160699800-160701200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr3:160700000-160700200	Enhancers	Adipose Nuclei	Adipose
17	chr3:160700000-160700400	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr3:160700000-160702000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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