Variant report

Variant	rs9844862
Chromosome Location	chr3:161076188-161076189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:64035675..64038032-chr3:161075125..161077341,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10513564	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs10936227	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11710489	0.88[EUR][1000 genomes]
rs11711413	0.82[EUR][1000 genomes]
rs11711695	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11715591	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs11718905	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs11929238	0.85[EUR][1000 genomes]
rs13059340	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs13059386	0.81[EUR][1000 genomes]
rs13062740	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs13073147	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs13076251	0.88[EUR][1000 genomes]
rs13084731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382429	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1450519	0.88[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1450521	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1450522	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1450523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478566	0.84[EUR][1000 genomes]
rs16832082	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2054710	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2100238	0.85[EUR][1000 genomes]
rs2122527	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404341	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2404342	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs34016896	0.82[EUR][1000 genomes]
rs34771618	0.85[EUR][1000 genomes]
rs34896809	0.85[EUR][1000 genomes]
rs34972965	0.81[EUR][1000 genomes]
rs35100811	0.88[EUR][1000 genomes]
rs4856701	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs4856703	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs4856756	0.82[EUR][1000 genomes]
rs4856757	0.82[EUR][1000 genomes]
rs4856769	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs60625846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441374	0.83[CEU][hapmap]
rs67460515	0.88[EUR][1000 genomes]
rs6780536	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7610800	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7610985	0.86[EUR][1000 genomes]
rs7630356	0.82[EUR][1000 genomes]
rs7647118	0.81[EUR][1000 genomes]
rs7647374	0.81[EUR][1000 genomes]
rs7648279	0.81[EUR][1000 genomes]

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	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
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9844862	SPTSSB	cis	Thyroid	GTEx
rs9844862	SPTSSB	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161059800-161089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:161064400-161083000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:161068200-161083200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:161068400-161083200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:161068800-161079000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:161071600-161077000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:161075000-161076200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:161075200-161076200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:161075400-161076200	Enhancers	NHEK	skin
10	chr3:161075600-161076200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:161075600-161076600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:161075800-161076200	Enhancers	Esophagus	oesophagus
13	chr3:161076000-161077400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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