Variant report

Variant	rs12553327
Chromosome Location	chr9:71512824-71512825
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11144167	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11144206	0.91[ASN][1000 genomes]
rs11999960	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12003432	0.91[ASN][1000 genomes]
rs12005037	0.84[AMR][1000 genomes]
rs12551225	0.85[AMR][1000 genomes]
rs12553357	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12555750	0.84[AMR][1000 genomes]
rs17391596	0.84[AMR][1000 genomes]
rs17391840	0.86[AMR][1000 genomes]
rs17392861	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17482797	0.83[AMR][1000 genomes]
rs17483533	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34483859	0.86[AMR][1000 genomes]
rs4120640	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4626674	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4745375	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55671140	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55830509	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55845142	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61221055	0.83[AMR][1000 genomes]
rs66460517	0.82[AMR][1000 genomes]
rs66883415	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72717935	0.83[AMR][1000 genomes]
rs72717955	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72720038	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73443515	0.81[ASN][1000 genomes]
rs73457664	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73461629	1.00[ASN][1000 genomes]
rs73461643	1.00[ASN][1000 genomes]
rs883951	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv614549	chr9:71506459-71659280	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12553327	PIP5K1B	cis	Artery Tibial	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71459000-71519200	Weak transcription	Colonic Mucosa	Colon
2	chr9:71460800-71517000	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr9:71492400-71515000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:71496600-71515200	Weak transcription	HepG2	liver
5	chr9:71502600-71516600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr9:71508800-71515200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:71509200-71514600	Enhancers	Fetal Heart	heart
8	chr9:71509600-71513000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr9:71509800-71514000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr9:71510400-71513200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:71510400-71513800	Strong transcription	Fetal Intestine Large	intestine
12	chr9:71510400-71513800	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr9:71510400-71514200	Enhancers	Right Ventricle	heart
14	chr9:71510400-71576200	Weak transcription	Stomach Mucosa	stomach
15	chr9:71510600-71515000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:71510600-71532400	Weak transcription	Small Intestine	intestine
17	chr9:71510800-71519800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:71511000-71514000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:71511000-71514200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:71511200-71513400	Weak transcription	Aorta	Aorta
21	chr9:71511200-71513800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr9:71511200-71514200	Enhancers	Fetal Muscle Leg	muscle
23	chr9:71511200-71514400	Enhancers	Right Atrium	heart
24	chr9:71511200-71519200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:71511400-71513000	Enhancers	Gastric	stomach
26	chr9:71511400-71513800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr9:71511400-71514200	Enhancers	Left Ventricle	heart
28	chr9:71511600-71513000	Enhancers	Fetal Muscle Trunk	muscle
29	chr9:71511600-71513400	Enhancers	Adipose Nuclei	Adipose
30	chr9:71511600-71514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr9:71511600-71514000	Weak transcription	Brain Hippocampus Middle	brain
32	chr9:71511600-71519800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:71511800-71513600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:71511800-71513800	Genic enhancers	Primary B cells from cord blood	blood
35	chr9:71511800-71514000	Weak transcription	Ovary	ovary
36	chr9:71511800-71519200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr9:71512000-71513000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr9:71512000-71514000	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr9:71512000-71514000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:71512000-71519800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:71512000-71520000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr9:71512200-71513200	Weak transcription	Lung	lung
43	chr9:71512200-71513400	Weak transcription	GM12878-XiMat	blood
44	chr9:71512200-71548800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:71512400-71513400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr9:71512400-71513600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr9:71512400-71517600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr9:71512400-71520200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr9:71512600-71513000	Bivalent Enhancer	Fetal Stomach	stomach
50	chr9:71512600-71513800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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