Variant report

Variant	rs9332465
Chromosome Location	chr5:177890055-177890056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177887745..177890184-chr5:177903224..177905118,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10051479	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10053433	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10078495	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11746672	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs12516264	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12652427	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12657817	0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs13159176	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs13179385	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1498617	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1846371	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2133281	0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2546626	0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs477842	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6601239	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs67405022	0.81[ASN][1000 genomes]
rs678011	0.83[ASN][1000 genomes]
rs6867956	0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6881003	0.85[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7725796	0.81[ASN][1000 genomes]
rs7726272	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv427739	chr5:177766033-177966666	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
6	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv883213	chr5:177811754-177947771	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv462570	chr5:177860454-178010145	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv600423	chr5:177860454-178010145	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1029822	chr5:177872333-177931889	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1033039	chr5:177873974-177926244	Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv537971	chr5:177873974-177926244	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1030915	chr5:177880081-177934927	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9332465	ZNF454	cis	parietal	SCAN
rs9332465	MSX2	cis	cerebellum	SCAN
rs9332465	NSD1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177877600-177894200	Weak transcription	Spleen	Spleen
2	chr5:177877800-177895400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:177887200-177896600	Enhancers	Fetal Stomach	stomach
4	chr5:177887600-177890600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr5:177887800-177897600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr5:177888000-177890400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr5:177888000-177890400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr5:177888000-177890600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr5:177888000-177890800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr5:177888000-177894400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr5:177888400-177891200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr5:177888400-177892400	Weak transcription	Fetal Lung	lung
13	chr5:177888400-177893600	Weak transcription	Pancreas	Pancrea
14	chr5:177888600-177890200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:177888600-177890400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:177888600-177893400	Weak transcription	Lung	lung
17	chr5:177888600-177893800	Weak transcription	Liver	Liver
18	chr5:177888600-177894000	Weak transcription	Fetal Intestine Small	intestine
19	chr5:177888600-177894200	Weak transcription	Right Ventricle	heart
20	chr5:177888600-177895200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:177888800-177893000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:177888800-177893800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:177888800-177894200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:177889000-177893600	Weak transcription	Fetal Thymus	thymus
25	chr5:177889200-177894200	Weak transcription	Left Ventricle	heart
26	chr5:177889200-177895200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:177889400-177892200	Weak transcription	Fetal Heart	heart
28	chr5:177889600-177890800	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr5:177889800-177890200	Active TSS	NHDF-Ad	bronchial
30	chr5:177889800-177890600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr5:177889800-177891000	Enhancers	H1 Cell Line	embryonic stem cell
32	chr5:177890000-177890200	Enhancers	H9 Cell Line	embryonic stem cell
33	chr5:177890000-177890200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr5:177890000-177890200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr5:177890000-177891200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr5:177890000-177892200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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