Variant report

Variant	rs9822435
Chromosome Location	chr3:160748068-160748069
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160746924..160750622-chr3:160787755..160791172,3	MCF-7	breast:
2	chr3:160739507..160741947-chr3:160747617..160749551,2	MCF-7	breast:
3	chr3:160746769..160748964-chr3:160821024..160822898,2	MCF-7	breast:
4	chr3:160745725..160748261-chr3:160752866..160755134,2	MCF-7	breast:
5	chr3:160747461..160750414-chr3:161128370..161130411,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169255	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10433352	0.81[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11711152	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs11713093	0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs11715733	0.95[AMR][1000 genomes]
rs11717272	0.90[CEU][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11718966	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs11720263	0.90[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11922957	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11922959	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12696112	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12696113	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13060601	0.81[EUR][1000 genomes]
rs13060718	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13062651	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13071892	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13071999	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs13073059	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs13085336	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs13098896	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13256	0.90[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1345156	1.00[CEU][hapmap]
rs1374787	0.86[JPT][hapmap]
rs1447610	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs1447622	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs1562464	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1599388	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16831796	0.81[CEU][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16831886	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1868105	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1868107	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs2014810	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2044571	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs2889390	0.80[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs34221255	0.83[AMR][1000 genomes]
rs34630898	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35914913	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4494975	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4521287	0.90[CEU][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4679920	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs4679929	0.92[AMR][1000 genomes]
rs4856700	0.80[CEU][hapmap]
rs57145341	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441338	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs6441362	0.81[EUR][1000 genomes]
rs6768115	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs6772723	0.90[CEU][hapmap];0.83[CHB][hapmap]
rs6774725	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs6794882	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6801444	1.00[CEU][hapmap]
rs6806015	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs68166680	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73021215	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73023235	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7433918	0.85[AMR][1000 genomes]
rs7610432	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7618455	0.84[AMR][1000 genomes]
rs7618924	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7624185	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7628389	0.81[CEU][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7641892	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs898677	0.81[CEU][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs935497	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs964533	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9812507	1.00[CEU][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9832109	1.00[CEU][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9844267	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs9845943	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs9857482	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs9857855	0.85[CEU][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9860537	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9862086	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9876142	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9880269	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9883566	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9822435	SPTSSB	cis	Thyroid	GTEx
rs9822435	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160745200-160748800	Weak transcription	Placenta	Placenta
2	chr3:160745200-160782600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:160746600-160749000	Weak transcription	Psoas Muscle	Psoas
4	chr3:160747600-160748200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links