Variant report

Variant	rs17302448
Chromosome Location	chr15:59941722-59941723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59862565..59864244-chr15:59938828..59941762,2	K562	blood:
2	chr15:59931535..59934345-chr15:59941225..59942727,2	K562	blood:
3	chr15:59940140..59943564-chr15:59947807..59951732,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140307	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12050786	0.95[EUR][1000 genomes]
rs16941544	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17236713	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]
rs17236734	0.87[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[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];0.87[ASN][1000 genomes]
rs28422085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28437066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28642859	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28654927	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28883924	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4775192	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4775193	0.93[CHB][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4775198	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6151443	0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs6151457	0.94[JPT][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs6151492	0.85[EUR][1000 genomes]
rs6151497	0.97[GIH][hapmap];0.89[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[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]
rs6151567	0.87[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6151575	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151591	0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7178008	0.84[EUR][1000 genomes]
rs8027421	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8033208	0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8033718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17302448	GCNT3	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59905200-59946200	Weak transcription	Gastric	stomach
2	chr15:59920600-59947000	Weak transcription	Small Intestine	intestine
3	chr15:59925000-59943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:59925600-59948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:59925800-59943800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:59926600-59944000	Weak transcription	Fetal Kidney	kidney
7	chr15:59926600-59947600	Weak transcription	Right Ventricle	heart
8	chr15:59926600-59948000	Weak transcription	Brain Angular Gyrus	brain
9	chr15:59927200-59948800	Weak transcription	Aorta	Aorta
10	chr15:59927400-59943800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:59927800-59942800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:59928400-59945600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:59928800-59942000	Weak transcription	Fetal Heart	heart
14	chr15:59929000-59942200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:59929000-59944000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:59929000-59947200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:59929200-59947600	Weak transcription	Ovary	ovary
18	chr15:59929600-59942400	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:59929600-59945800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr15:59929800-59946400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:59930600-59948200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:59932800-59947800	Weak transcription	Colonic Mucosa	Colon
23	chr15:59932800-59948000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:59934400-59942400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:59935200-59943600	Weak transcription	Stomach Mucosa	stomach
26	chr15:59935600-59944200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:59935800-59944200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:59935800-59945000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:59936000-59944200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr15:59936000-59945600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:59936000-59946000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr15:59936000-59948000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:59936200-59946600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr15:59936400-59941800	Strong transcription	Hela-S3	cervix
35	chr15:59936400-59946800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:59936400-59946800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr15:59936400-59947000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:59936600-59943000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:59936600-59944000	Strong transcription	Adipose Nuclei	Adipose
40	chr15:59936600-59945000	Strong transcription	NHDF-Ad	bronchial
41	chr15:59936600-59945200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:59936600-59945800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr15:59936600-59946800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr15:59936600-59946800	Strong transcription	Dnd41	blood
45	chr15:59936600-59947000	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr15:59937000-59946200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:59937200-59942200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr15:59937400-59947600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:59937600-59944000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr15:59937600-59944000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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