Variant report

Variant	rs10981297
Chromosome Location	chr9:99998646-99998647
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:99994939..99996604-chr9:99997527..100000515,2	MCF-7	breast:
2	chr9:99998207..100000626-chr9:100147568..100149189,2	K562	blood:
3	chr13:41495372..41498388-chr9:99998502..100001030,4	K562	blood:
4	chr13:41495372..41496932-chr9:99998502..100000578,3	K562	blood:

Variant related genes	Relation type
ENSG00000168852	Chromatin interaction
ENSG00000239827	Chromatin interaction
ENSG00000235494	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1048451	0.94[CEU][hapmap]
rs10521029	0.94[CEU][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10759527	0.95[JPT][hapmap]
rs10817273	0.91[JPT][hapmap]
rs10817286	0.91[JPT][hapmap]
rs10817491	0.94[CEU][hapmap]
rs10817504	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs10981158	0.85[AFR][1000 genomes]
rs10981161	0.87[AFR][1000 genomes]
rs10981367	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10981460	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap]
rs10981784	0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs10981800	0.94[CEU][hapmap]
rs11581	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs12377538	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap]
rs12378350	0.87[ASW][hapmap];0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap]
rs12550923	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12551740	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap]
rs12552659	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap]
rs12553213	0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap]
rs12554363	0.94[CEU][hapmap];0.88[YRI][hapmap]
rs12554887	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12555277	0.94[CEU][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap]
rs13285567	0.85[CEU][hapmap]
rs13286510	0.94[CEU][hapmap]
rs13287082	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13289134	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13289813	0.94[CEU][hapmap]
rs13292715	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13300328	0.94[CEU][hapmap]
rs13301045	0.93[CEU][hapmap];0.80[YRI][hapmap]
rs1531440	0.87[ASW][hapmap];0.88[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap]
rs1564048	0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs16919675	0.88[CEU][hapmap]
rs1986462	1.00[CEU][hapmap]
rs2045729	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap]
rs2045730	0.94[CEU][hapmap]
rs2045731	0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap]
rs2290933	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap]
rs2306090	0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap]
rs2306092	0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap]
rs2306094	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap]
rs2401384	0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs34476799	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34754033	0.87[AMR][1000 genomes]
rs34868501	0.81[AFR][1000 genomes]
rs35590659	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3747490	0.94[CEU][hapmap]
rs3747491	0.94[CEU][hapmap]
rs3747492	0.94[CEU][hapmap];0.83[YRI][hapmap]
rs3747495	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap]
rs3747498	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs3747499	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap]
rs3747504	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs3747506	0.87[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs3994560	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap]
rs4128763	1.00[CEU][hapmap]
rs4742688	0.94[CEU][hapmap];0.83[YRI][hapmap]
rs4743070	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4743073	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4743082	0.87[ASW][hapmap];0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap]
rs4743083	0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs4743085	0.94[CEU][hapmap]
rs4743086	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs62556659	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62559861	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6478038	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6478039	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7020530	0.94[CEU][hapmap];0.82[AMR][1000 genomes]
rs7038496	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap]
rs7041222	0.94[CEU][hapmap]
rs7848439	0.87[AFR][1000 genomes]
rs898869	0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap]
rs898870	0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10981297	VN1R51P	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99992200-99999600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:99994800-99999000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:99995600-99999000	Weak transcription	HepG2	liver
4	chr9:99995600-99999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr9:99995600-99999800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr9:99995800-99999000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:99995800-99999600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:99995800-99999600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:99996000-99999000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:99996000-99999600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:99996200-99999200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:99996600-99999000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:99998200-99999000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr9:99998400-99998800	Enhancers	H9 Cell Line	embryonic stem cell
15	chr9:99998400-99999200	Enhancers	Dnd41	blood
16	chr9:99998400-100001800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:99998600-99998800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr9:99998600-99999200	Weak transcription	K562	blood
19	chr9:99998600-100002200	Active TSS	iPS-20b Cell Line	embryonic stem cell

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