Variant report

Variant	rs11078389
Chromosome Location	chr17:17478352-17478353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17478310..17481534-chr17:17481749..17484707,3	K562	blood:
2	chr17:17478222..17479818-chr17:17481542..17483220,2	MCF-7	breast:
3	chr17:17477958..17480343-chr17:17481863..17484707,3	K562	blood:

Variant related genes	Relation type
ENSG00000206730	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11651620	0.81[CEU][hapmap]
rs11654842	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11656215	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11867345	1.00[ASN][1000 genomes]
rs11871667	0.94[ASN][1000 genomes]
rs12939945	1.00[ASN][1000 genomes]
rs12945144	0.96[ASN][1000 genomes]
rs12948060	1.00[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1531100	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2124344	1.00[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4244593	0.81[CEU][hapmap]
rs4244596	1.00[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4244598	1.00[CEU][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646340	0.88[CEU][hapmap]
rs4646341	0.88[CEU][hapmap]
rs4646346	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646347	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4646349	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646350	1.00[CEU][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646351	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646352	1.00[ASN][1000 genomes]
rs4646356	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4646357	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4646358	1.00[ASN][1000 genomes]
rs4646359	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4646365	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4646368	1.00[ASN][1000 genomes]
rs4646369	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646370	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4646372	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4646385	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4646387	0.81[CEU][hapmap]
rs4646388	0.97[ASN][1000 genomes]
rs4646389	0.81[CEU][hapmap]
rs4646390	0.82[CEU][hapmap]
rs4646391	0.81[CEU][hapmap]
rs4646392	0.81[CEU][hapmap]
rs4646396	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4646402	0.81[CEU][hapmap]
rs6502603	0.80[CEU][hapmap]
rs7209113	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7221487	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs729974	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs729975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744925	1.00[ASN][1000 genomes]
rs746899	0.81[CEU][hapmap]
rs747770	0.85[CEU][hapmap]
rs750546	0.88[CEU][hapmap]
rs8079427	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8082417	1.00[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs897450	1.00[ASN][1000 genomes]
rs897451	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs936108	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9894588	0.95[ASN][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
rs11078389	SNORD49B	cis	parietal	SCAN
rs11078389	RAI1	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17436800-17479200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr17:17465600-17484000	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr17:17466000-17484000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr17:17466400-17480000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr17:17468800-17482800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr17:17468800-17484000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:17468800-17484000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr17:17469000-17478400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:17469000-17478600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr17:17469000-17482000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr17:17469000-17494000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:17469200-17493600	Weak transcription	Thymus	Thymus
13	chr17:17469600-17483800	Weak transcription	Osteobl	bone
14	chr17:17469800-17478600	Weak transcription	NHLF	lung
15	chr17:17470200-17483800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr17:17470800-17478400	Weak transcription	Aorta	Aorta
17	chr17:17470800-17483600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr17:17471400-17479600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr17:17471600-17482800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr17:17471600-17493600	Weak transcription	Brain Angular Gyrus	brain
21	chr17:17471800-17478400	Weak transcription	Brain Substantia Nigra	brain
22	chr17:17471800-17478800	Weak transcription	Fetal Lung	lung
23	chr17:17471800-17479000	Weak transcription	Brain Hippocampus Middle	brain
24	chr17:17471800-17479600	Weak transcription	Brain Anterior Caudate	brain
25	chr17:17471800-17493600	Weak transcription	Colon Smooth Muscle	Colon
26	chr17:17472200-17478400	Weak transcription	Colonic Mucosa	Colon
27	chr17:17472200-17478400	Weak transcription	Gastric	stomach
28	chr17:17472200-17478600	Weak transcription	Esophagus	oesophagus
29	chr17:17472400-17493600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr17:17473000-17479600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr17:17473200-17478600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:17473600-17484000	Weak transcription	HSMMtube	muscle
33	chr17:17473800-17478800	Weak transcription	Placenta	Placenta
34	chr17:17474200-17478600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr17:17474200-17493600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr17:17474400-17478400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr17:17474400-17479000	Weak transcription	Brain Germinal Matrix	brain
38	chr17:17474400-17481200	Strong transcription	Fetal Stomach	stomach
39	chr17:17474600-17493800	Weak transcription	Primary B cells from cord blood	blood
40	chr17:17474800-17493200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:17475000-17478800	Weak transcription	Right Atrium	heart
42	chr17:17475000-17483200	Weak transcription	Stomach Mucosa	stomach
43	chr17:17475600-17478600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr17:17475600-17478800	Weak transcription	Fetal Heart	heart
45	chr17:17475600-17484400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr17:17475800-17478600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr17:17475800-17484000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr17:17476800-17478400	Weak transcription	Hela-S3	cervix
49	chr17:17476800-17480800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:17477000-17480600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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