Variant report

Variant	rs9547717
Chromosome Location	chr13:37579480-37579481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:37572075-37586589	K562	blood:	n/a	n/a
2	POLR2A	chr13:37579070-37580251	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
EXOSC8	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1199962	0.81[CEU][hapmap]
rs1199963	0.81[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs1199974	0.81[CEU][hapmap]
rs1199981	0.81[CEU][hapmap]
rs1199982	0.81[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs1199983	0.81[CEU][hapmap]
rs1199984	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs12865199	0.87[EUR][1000 genomes]
rs1543738	0.81[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap]
rs1764483	0.81[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs1924419	0.95[EUR][1000 genomes]
rs1924420	0.94[EUR][1000 genomes]
rs1924422	0.91[CEU][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs1937761	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs2093817	0.81[CEU][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs2147169	0.91[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2181787	0.91[EUR][1000 genomes]
rs2181788	0.82[CEU][hapmap]
rs2186157	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2323165	0.91[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2769541	0.90[CEU][hapmap]
rs2785620	0.81[CEU][hapmap];1.00[GIH][hapmap]
rs4291799	0.91[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs483304	0.80[EUR][1000 genomes]
rs4941854	0.91[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4941855	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4941856	0.91[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs4943441	0.81[CEU][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs568992	0.84[EUR][1000 genomes]
rs587505	0.91[CEU][hapmap];0.88[TSI][hapmap]
rs6563506	0.82[CEU][hapmap]
rs6563507	0.91[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6563508	0.81[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs675108	0.82[CEU][hapmap]
rs688280	0.91[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap]
rs71432622	0.83[EUR][1000 genomes]
rs7317750	0.91[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs7321129	0.91[CEU][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs7329314	0.95[EUR][1000 genomes]
rs7334233	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7338929	0.91[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs7982674	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7983986	0.91[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs7984730	0.91[EUR][1000 genomes]
rs7989205	0.91[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs7989380	0.81[CEU][hapmap]
rs7991057	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7991181	0.95[EUR][1000 genomes]
rs7997310	0.81[CEU][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs9315458	0.92[EUR][1000 genomes]
rs9315459	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9531998	0.95[EUR][1000 genomes]
rs9532001	0.91[CEU][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs9532002	0.95[EUR][1000 genomes]
rs9532004	0.91[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs9532005	0.91[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9547703	0.82[CEU][hapmap]
rs9547704	0.82[CEU][hapmap]
rs9547707	0.91[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs9547712	0.95[EUR][1000 genomes]
rs9547715	0.91[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs9547718	0.91[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs9576153	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9576154	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9594181	0.95[EUR][1000 genomes]
rs9603121	0.91[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.92[EUR][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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv522336	chr13:37305641-37584838	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv977365	chr13:37576107-37580409	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9547717	SUPT20H	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37575400-37580600	Weak transcription	Small Intestine	intestine
2	chr13:37575400-37583800	Weak transcription	Spleen	Spleen
3	chr13:37575400-37631200	Weak transcription	Stomach Mucosa	stomach
4	chr13:37575600-37583800	Weak transcription	Esophagus	oesophagus
5	chr13:37575600-37583800	Weak transcription	Gastric	stomach
6	chr13:37575600-37592800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:37576000-37580600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr13:37576000-37581000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr13:37576000-37581000	Weak transcription	Psoas Muscle	Psoas
10	chr13:37576000-37582400	Weak transcription	Colonic Mucosa	Colon
11	chr13:37576000-37583800	Weak transcription	Pancreas	Pancrea
12	chr13:37576000-37592600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr13:37576200-37579600	Weak transcription	Brain Anterior Caudate	brain
14	chr13:37576200-37580600	Weak transcription	Fetal Kidney	kidney
15	chr13:37576200-37581400	Weak transcription	Fetal Brain Male	brain
16	chr13:37576200-37606200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr13:37576200-37623800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr13:37576400-37580800	Weak transcription	Brain Angular Gyrus	brain
19	chr13:37576400-37581000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr13:37576400-37581600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr13:37576400-37582200	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr13:37576400-37582400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr13:37576400-37583800	Weak transcription	Fetal Heart	heart
24	chr13:37576400-37588600	Weak transcription	Hela-S3	cervix
25	chr13:37576400-37595400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr13:37576400-37607600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr13:37576400-37608600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:37576400-37618800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr13:37576400-37623800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr13:37576600-37582400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr13:37576600-37586800	Strong transcription	HSMM	muscle
32	chr13:37576600-37587400	Strong transcription	Placenta	Placenta
33	chr13:37576600-37600400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr13:37576600-37608400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr13:37576600-37623000	Strong transcription	Liver	Liver
36	chr13:37576600-37625800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr13:37576800-37581800	Genic enhancers	Dnd41	blood
38	chr13:37576800-37584400	Strong transcription	NHEK	skin
39	chr13:37576800-37586200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr13:37576800-37588400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr13:37576800-37600600	Strong transcription	HUVEC	blood vessel
42	chr13:37576800-37603000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr13:37576800-37609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr13:37576800-37621200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr13:37576800-37623200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr13:37577000-37580800	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr13:37577000-37582000	Strong transcription	A549	lung
48	chr13:37577000-37584200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr13:37577000-37585000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr13:37577000-37585400	Strong transcription	Fetal Lung	lung

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