Variant report

Variant	rs12377244
Chromosome Location	chr9:99976006-99976007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1048451	0.94[CEU][hapmap]
rs10521028	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10521029	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs10817491	0.94[CEU][hapmap]
rs10817504	0.82[CEU][hapmap]
rs10980890	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10980955	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10980992	0.89[EUR][1000 genomes]
rs10981005	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10981158	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10981161	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981297	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10981367	0.94[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap]
rs10981460	0.94[CEU][hapmap]
rs10981784	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs10981800	0.94[CEU][hapmap]
rs11581	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs12377538	0.94[CEU][hapmap]
rs12378350	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs12378555	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12550862	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12550923	0.94[CEU][hapmap]
rs12551740	0.94[CEU][hapmap]
rs12552659	0.93[CEU][hapmap]
rs12553213	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs12554363	0.94[CEU][hapmap]
rs12555277	0.94[CEU][hapmap]
rs12555636	0.86[AMR][1000 genomes]
rs13285567	0.85[CEU][hapmap]
rs13286510	0.94[CEU][hapmap]
rs13286601	0.84[ASN][1000 genomes]
rs13287082	0.94[CEU][hapmap]
rs13287095	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13289134	0.94[CEU][hapmap]
rs13289813	0.94[CEU][hapmap]
rs13300328	0.94[CEU][hapmap]
rs13301045	0.93[CEU][hapmap]
rs1531440	0.88[CEU][hapmap];0.97[GIH][hapmap];0.96[TSI][hapmap]
rs1564048	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs16905669	0.88[EUR][1000 genomes]
rs16919675	0.88[CEU][hapmap]
rs1857085	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1986462	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2045729	0.94[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap]
rs2045730	0.94[CEU][hapmap]
rs2045731	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs2306090	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs2306092	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs2306094	0.94[CEU][hapmap]
rs2401384	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs34592472	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34868501	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35241252	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35285539	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3747490	0.94[CEU][hapmap]
rs3747491	0.94[CEU][hapmap]
rs3747492	0.94[CEU][hapmap]
rs3747495	0.94[CEU][hapmap];0.97[GIH][hapmap];0.96[TSI][hapmap]
rs3747498	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap]
rs3747499	0.94[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap]
rs3747504	0.94[CEU][hapmap];0.97[GIH][hapmap];0.96[TSI][hapmap]
rs3747506	0.88[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap]
rs3994560	0.94[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap]
rs4014782	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4128763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4463540	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742688	0.94[CEU][hapmap]
rs4743061	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743062	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743070	0.94[CEU][hapmap]
rs4743073	0.94[CEU][hapmap]
rs4743082	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs4743083	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs4743085	0.94[CEU][hapmap]
rs4743086	0.94[CEU][hapmap]
rs56860287	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58003970	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7018753	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7020530	0.94[CEU][hapmap]
rs7021506	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7038496	0.94[CEU][hapmap]
rs7041222	0.94[CEU][hapmap]
rs7848439	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7851025	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7860303	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7865758	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs898869	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs898870	0.94[CEU][hapmap];0.96[TSI][hapmap]

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	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv893607	chr9:99906545-99996548	Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv972433	chr9:99962059-99983443	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12377244	VN1R51P	cis	Thyroid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99968200-99976800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:99968200-99976800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:99974600-99977000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:99975400-99976200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr9:99976000-99976200	Genic enhancers	H1 Cell Line	embryonic stem cell
6	chr9:99976000-99976200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr9:99976000-99976600	Enhancers	H9 Cell Line	embryonic stem cell
8	chr9:99976000-99976600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr9:99976000-99976600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr9:99976000-99976600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr9:99976000-99976800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr9:99976000-99976800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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