Variant report

Variant	rs9372547
Chromosome Location	chr6:119994317-119994318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1040656	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11153841	0.90[EUR][1000 genomes]
rs1159767	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1160757	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12154173	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1341496	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1341500	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1341501	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1341503	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1884255	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1884256	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs2064568	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064569	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2144360	0.90[EUR][1000 genomes]
rs6569084	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6913189	0.81[ASN][1000 genomes]
rs6913597	0.88[ASN][1000 genomes]
rs6916609	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6930071	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6933847	0.88[ASN][1000 genomes]
rs6939299	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs706858	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs767398	0.81[AFR][1000 genomes]
rs7757918	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7758447	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7772968	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7776137	0.81[ASN][1000 genomes]
rs807310	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs807311	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9320699	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320702	0.84[ASN][1000 genomes]
rs9372545	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9372546	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9374815	0.81[AFR][1000 genomes]
rs9374816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374818	0.86[ASN][1000 genomes]
rs9385082	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9385083	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9387664	0.90[EUR][1000 genomes]
rs9387668	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9387669	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9387670	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9387672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9387678	0.80[EUR][1000 genomes]
rs9387679	0.80[EUR][1000 genomes]
rs9398521	0.81[AFR][1000 genomes]
rs9401162	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9481955	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9489765	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1027904	chr6:119709488-120001986	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv533518	chr6:119712186-119998618	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3442553	chr6:119742069-120076777	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1027370	chr6:119869409-120056608	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538431	chr6:119869409-120056608	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9372547	SERINC1	cis	cerebellum	SCAN
rs9372547	NT5DC1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119991800-119995000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:119991800-120008000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:119992200-119995000	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr6:119992200-119995200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr6:119992800-120009600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:119993400-119994400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:119993400-119994800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:119993600-119994400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:119993800-119994400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr6:119993800-119994400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:119993800-119994800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:119994000-119995600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr6:119994200-119994400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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