Variant report

Variant	rs17391596
Chromosome Location	chr9:71421343-71421344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:73160073..73160620-chr9:71420702..71421682,2	NB4	blood:
2	chr3:73158387..73161479-chr9:71419682..71422682,3	K562	blood:
3	chr3:73160048..73160628-chr9:71420682..71421702,10	HCT-116	colon:
4	chr3:73159867..73160571-chr9:71420682..71421682,2	Hela-S3	cervix:
5	chr9:71420662..71423189-chr9:71425741..71428511,3	K562	blood:
6	chr9:71398048..71400496-chr9:71420484..71423422,2	K562	blood:
7	chr17:41398972..41401127-chr9:71419682..71422702,5	K562	blood:

Variant related genes	Relation type
ENSG00000223247	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10511965	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10735625	0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs10746925	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10869327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10869422	0.83[MEX][hapmap]
rs11143793	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs11144167	0.81[AMR][1000 genomes]
rs11999960	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12338444	0.80[ASN][1000 genomes]
rs12551225	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553327	0.84[AMR][1000 genomes]
rs12555750	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1537885	0.87[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17391162	0.82[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17391840	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17392861	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17482181	0.87[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17482797	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17483533	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4120640	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4626674	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4745375	0.83[MEX][hapmap]
rs55671140	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55830509	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55845142	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60373811	0.84[ASN][1000 genomes]
rs61221055	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6560397	0.84[MEX][hapmap]
rs66460517	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66883415	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67047473	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67457572	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7018552	0.87[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7031263	0.83[TSI][hapmap]
rs7037030	0.87[ASN][1000 genomes]
rs7044460	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72717927	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72717935	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717955	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720038	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73457664	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871676	0.82[CEU][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7875396	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs945575	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs952590	0.82[CEU][hapmap]
rs972059	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1050741	chr9:71405224-71450033	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv540148	chr9:71405224-71450033	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
13	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17391596	PIP5K1B	cis	parietal	SCAN
rs17391596	PIP5K1B	cis	Artery Tibial	GTEx
rs17391596	TJP2	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71404600-71431400	Weak transcription	HepG2	liver
2	chr9:71410200-71428600	Weak transcription	Aorta	Aorta
3	chr9:71414000-71437000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:71414000-71445000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:71416600-71422000	Enhancers	Primary B cells from peripheral blood	blood
6	chr9:71417400-71421800	Enhancers	Right Ventricle	heart
7	chr9:71417400-71423600	Enhancers	Left Ventricle	heart
8	chr9:71418600-71421400	Weak transcription	Colonic Mucosa	Colon
9	chr9:71418600-71444800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:71419600-71421800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr9:71419600-71422200	Genic enhancers	Primary B cells from cord blood	blood
12	chr9:71419800-71421600	Enhancers	Gastric	stomach
13	chr9:71419800-71421800	Enhancers	Fetal Muscle Leg	muscle
14	chr9:71419800-71421800	Enhancers	Pancreas	Pancrea
15	chr9:71419800-71422200	Enhancers	Rectal Smooth Muscle	rectum
16	chr9:71420000-71421400	Enhancers	Lung	lung
17	chr9:71420000-71421600	Enhancers	Right Atrium	heart
18	chr9:71420200-71421600	Enhancers	K562	blood
19	chr9:71420200-71422600	Enhancers	Fetal Stomach	stomach
20	chr9:71420400-71421800	Genic enhancers	Fetal Intestine Large	intestine
21	chr9:71420600-71421400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr9:71420600-71421400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr9:71420600-71421400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr9:71420600-71422600	Enhancers	GM12878-XiMat	blood
25	chr9:71420800-71421400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:71420800-71421400	Enhancers	Fetal Kidney	kidney
27	chr9:71420800-71421400	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr9:71420800-71422800	Enhancers	Colon Smooth Muscle	Colon
29	chr9:71420800-71424200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:71420800-71434600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:71421000-71421400	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr9:71421000-71421600	Enhancers	Placenta	Placenta
33	chr9:71421000-71422200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:71421000-71424600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:71421000-71431800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr9:71421000-71437600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:71421200-71421400	Flanking Active TSS	Fetal Heart	heart
38	chr9:71421200-71421800	Strong transcription	Fetal Intestine Small	intestine
39	chr9:71421200-71424000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:71421200-71426000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:71421200-71437200	Weak transcription	Stomach Mucosa	stomach
42	chr9:71421200-71437600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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