Variant report

Variant	rs17236713
Chromosome Location	chr15:59948997-59948998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59680945..59682711-chr15:59948219..59950781,2	MCF-7	breast:
2	chr15:59948214..59950768-chr15:59963899..59966386,2	K562	blood:
3	chr15:59947605..59950537-chr15:59979625..59981765,3	MCF-7	breast:
4	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
5	chr15:59946363..59951356-chr15:59979923..59984049,7	K562	blood:

Variant related genes	Relation type
ENSG00000227161	Chromatin interaction
ENSG00000140299	Chromatin interaction
ENSG00000259238	Chromatin interaction
ENSG00000238767	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12050786	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16941544	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17236734	0.87[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17302448	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17302608	0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs28395445	0.95[EUR][1000 genomes]
rs28418513	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28422085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28437066	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28642859	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28654927	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28883924	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775193	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4775198	0.95[EUR][1000 genomes]
rs6151443	0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs6151457	0.94[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs6151492	0.85[EUR][1000 genomes]
rs6151497	0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs6151505	0.85[EUR][1000 genomes]
rs6151522	0.95[EUR][1000 genomes]
rs6151534	0.80[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes]
rs6151538	0.95[EUR][1000 genomes]
rs6151540	0.95[EUR][1000 genomes]
rs6151552	0.80[AFR][1000 genomes]
rs6151567	0.87[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151591	0.87[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7178008	0.84[EUR][1000 genomes]
rs8027421	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033208	0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8033718	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1043693	chr15:59944471-59971500	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17236713	GCNT3	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59938600-59949200	Weak transcription	Lung	lung
2	chr15:59941000-59949200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:59946800-59949000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr15:59947200-59949000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:59947400-59949000	Enhancers	Stomach Mucosa	stomach
6	chr15:59947600-59949000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr15:59947600-59949000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr15:59947600-59949000	Enhancers	Fetal Heart	heart
9	chr15:59947600-59950000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:59947600-59950200	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr15:59947600-59950200	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr15:59947600-59950400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:59947800-59949000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr15:59947800-59949000	Flanking Active TSS	Dnd41	blood
15	chr15:59947800-59949000	Flanking Active TSS	Hela-S3	cervix
16	chr15:59947800-59949200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:59947800-59949800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:59947800-59950200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:59948000-59949000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr15:59948000-59949000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:59948000-59949200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:59948000-59949200	Flanking Active TSS	Liver	Liver
23	chr15:59948000-59949200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr15:59948000-59949200	Flanking Active TSS	HUVEC	blood vessel
25	chr15:59948000-59949800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr15:59948200-59949000	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr15:59948200-59949000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr15:59948200-59949000	Flanking Active TSS	Fetal Brain Male	brain
29	chr15:59948200-59949000	Flanking Active TSS	Fetal Lung	lung
30	chr15:59948200-59949000	Flanking Active TSS	Rectal Smooth Muscle	rectum
31	chr15:59948200-59949000	Flanking Active TSS	K562	blood
32	chr15:59948200-59949000	Flanking Active TSS	NHEK	skin
33	chr15:59948200-59949200	Weak transcription	Esophagus	oesophagus
34	chr15:59948200-59949200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr15:59948200-59949400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:59948200-59950000	Active TSS	HSMM	muscle
37	chr15:59948200-59950200	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr15:59948200-59950200	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr15:59948400-59949000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:59948400-59949000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr15:59948400-59949000	Flanking Active TSS	Colonic Mucosa	Colon
42	chr15:59948400-59949000	Weak transcription	Left Ventricle	heart
43	chr15:59948400-59949000	Flanking Active TSS	NH-A	brain
44	chr15:59948400-59949200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:59948400-59949200	Weak transcription	Gastric	stomach
46	chr15:59948400-59949200	Weak transcription	Pancreas	Pancrea
47	chr15:59948400-59949200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr15:59948400-59949400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr15:59948400-59950000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:59948400-59950000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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