Variant report

Variant	rs9828553
Chromosome Location	chr3:151025568-151025569
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:151011307..151016157-chr3:151019117..151025599,7	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1048408	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10513392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714714	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11717955	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11719936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12330831	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12488267	0.88[ASN][1000 genomes]
rs12494865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1317465	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1352886	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1472122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565574	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16863323	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16863334	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16863336	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1844924	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1882014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1882015	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1882016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs1882017	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1920396	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1980143	0.89[CEU][hapmap]
rs28371419	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28497341	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2904430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4076581	0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs4475010	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4679772	0.89[CEU][hapmap]
rs4679783	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680254	0.82[CEU][hapmap]
rs4680257	0.89[CEU][hapmap]
rs4680260	0.81[CEU][hapmap]
rs56105302	0.94[ASN][1000 genomes]
rs56367650	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58334126	0.96[ASN][1000 genomes]
rs62283021	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6765215	0.94[ASN][1000 genomes]
rs6768130	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6782313	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6807308	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6809692	0.87[CEU][hapmap]
rs7617677	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7621113	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7621183	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7621211	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7623448	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7653603	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8180086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9757688	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9810067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9815520	0.89[CEU][hapmap]
rs9827619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9829753	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9870740	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9875152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9828553	SLC33A1	cis	parietal	SCAN
rs9828553	GPR171	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:151021600-151025800	Enhancers	Placenta	Placenta
3	chr3:151021600-151026600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:151022400-151025600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:151022400-151025800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr3:151022400-151026000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr3:151022400-151026200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:151022400-151026400	Enhancers	NHLF	lung
9	chr3:151022600-151026400	Enhancers	NHDF-Ad	bronchial
10	chr3:151022600-151026800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:151023200-151034600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:151023400-151027800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:151023600-151027000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr3:151023800-151026000	Enhancers	NH-A	brain
15	chr3:151024000-151025600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:151024000-151026400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr3:151024000-151026600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:151024000-151027200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:151024400-151027600	Enhancers	Hela-S3	cervix
20	chr3:151024400-151029000	Genic enhancers	HMEC	breast
21	chr3:151024600-151025600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:151024600-151025600	Weak transcription	Osteobl	bone
23	chr3:151024600-151026200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:151024600-151028200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:151024600-151029600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:151024600-151032600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:151024600-151032800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:151024800-151027800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:151024800-151030200	Genic enhancers	NHEK	skin
30	chr3:151025000-151025600	Enhancers	H9 Cell Line	embryonic stem cell
31	chr3:151025000-151025600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:151025000-151025800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr3:151025200-151025800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:151025200-151025800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:151025200-151030600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:151025200-151030800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:151025200-151030800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:151025200-151032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:151025400-151025600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:151025400-151025800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:151025400-151025800	Enhancers	Esophagus	oesophagus
42	chr3:151025400-151030600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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