Variant report

Variant	rs12948060
Chromosome Location	chr17:17477384-17477385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17460513..17462662-chr17:17475967..17478047,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11078389	1.00[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11651620	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11654842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12941371	0.85[ASN][1000 genomes]
rs1531100	0.88[CEU][hapmap]
rs2124344	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4244593	0.81[CEU][hapmap]
rs4244596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646340	0.88[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs4646341	0.88[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4646346	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4646347	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4646349	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4646350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646356	0.96[CEU][hapmap]
rs4646357	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646359	0.96[CEU][hapmap]
rs4646365	0.95[CEU][hapmap]
rs4646369	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4646370	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646372	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646387	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4646389	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4646390	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4646391	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4646392	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4646394	0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs4646395	0.89[ASN][1000 genomes]
rs4646402	0.81[CEU][hapmap]
rs6502603	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7209113	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221487	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729975	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs746899	0.81[CEU][hapmap]
rs747770	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs750546	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs8079427	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080165	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8082417	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs897451	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9892560	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9893179	0.89[ASN][1000 genomes]
rs9894321	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9894588	0.83[EUR][1000 genomes]
rs9895955	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv907744	chr17:17404586-17504856	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv907746	chr17:17412032-17478917	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv907747	chr17:17412032-17504856	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
6	nsv470579	chr17:17424332-17493810	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
9	nsv1062052	chr17:17461050-17507199	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv543237	chr17:17461050-17507199	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv833383	chr17:17464635-17509138	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12948060	SNORD49B	cis	parietal	SCAN
rs12948060	RAI1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17418200-17478000	Weak transcription	Primary T cells from cord blood	blood
2	chr17:17436800-17479200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:17453400-17477800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:17464200-17477800	Weak transcription	Dnd41	blood
5	chr17:17465600-17484000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr17:17465800-17478000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr17:17465800-17478000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr17:17465800-17478000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr17:17465800-17478000	Weak transcription	NHEK	skin
10	chr17:17465800-17478200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:17465800-17478200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr17:17465800-17478200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:17465800-17478200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:17466000-17484000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr17:17466400-17478200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr17:17466400-17480000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr17:17467200-17478200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr17:17468000-17478000	Weak transcription	A549	lung
19	chr17:17468800-17482800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr17:17468800-17484000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr17:17468800-17484000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr17:17469000-17478400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:17469000-17478600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr17:17469000-17482000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr17:17469000-17494000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr17:17469200-17493600	Weak transcription	Thymus	Thymus
27	chr17:17469600-17483800	Weak transcription	Osteobl	bone
28	chr17:17469800-17478600	Weak transcription	NHLF	lung
29	chr17:17470200-17483800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr17:17470600-17478200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:17470800-17478400	Weak transcription	Aorta	Aorta
32	chr17:17470800-17483600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr17:17471000-17478000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr17:17471200-17478000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:17471200-17478000	Weak transcription	Fetal Thymus	thymus
36	chr17:17471400-17478200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr17:17471400-17479600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr17:17471600-17482800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr17:17471600-17493600	Weak transcription	Brain Angular Gyrus	brain
40	chr17:17471800-17478400	Weak transcription	Brain Substantia Nigra	brain
41	chr17:17471800-17478800	Weak transcription	Fetal Lung	lung
42	chr17:17471800-17479000	Weak transcription	Brain Hippocampus Middle	brain
43	chr17:17471800-17479600	Weak transcription	Brain Anterior Caudate	brain
44	chr17:17471800-17493600	Weak transcription	Colon Smooth Muscle	Colon
45	chr17:17472200-17478000	Weak transcription	Lung	lung
46	chr17:17472200-17478400	Weak transcription	Colonic Mucosa	Colon
47	chr17:17472200-17478400	Weak transcription	Gastric	stomach
48	chr17:17472200-17478600	Weak transcription	Esophagus	oesophagus
49	chr17:17472400-17493600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr17:17473000-17479600	Weak transcription	Primary hematopoietic stem cells	blood

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