Variant report

Variant	rs4492445
Chromosome Location	chr9:72000164-72000165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71996842..72001188-chr9:72001690..72005051,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10115490	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10118562	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10746595	0.84[CEU][hapmap];0.81[GIH][hapmap];0.83[YRI][hapmap]
rs10746596	0.90[AFR][1000 genomes]
rs10780321	0.94[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10780324	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10780326	0.92[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10780333	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs10780336	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10867426	0.92[CEU][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10867436	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10867453	0.88[JPT][hapmap]
rs11138304	0.94[ASN][1000 genomes]
rs11138332	0.94[ASN][1000 genomes]
rs11138334	0.94[ASN][1000 genomes]
rs11138402	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11138412	0.90[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11138435	0.88[JPT][hapmap]
rs1334311	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829094	0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3892193	0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4112222	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.94[ASN][1000 genomes]
rs4255205	0.82[AFR][1000 genomes]
rs4421413	0.94[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.94[ASN][1000 genomes]
rs4458929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559495	0.88[CEU][hapmap];0.81[GIH][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs7024302	0.88[JPT][hapmap]
rs7035141	0.88[JPT][hapmap]
rs7047788	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7851643	0.94[ASN][1000 genomes]
rs7859544	0.94[ASN][1000 genomes]
rs7870082	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4492445	SPIRE2	trans	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71979000-72001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:71983400-72001800	Weak transcription	Brain Anterior Caudate	brain
3	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:71986600-72002600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:71989000-72002800	Weak transcription	Brain Substantia Nigra	brain
6	chr9:71990600-72000200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:71991800-72012200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:71992000-72001800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:71992000-72009800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:71992200-72001800	Weak transcription	Adipose Nuclei	Adipose
11	chr9:71992400-72001800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:71992600-72000800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:71992600-72006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:71992600-72006600	Weak transcription	Esophagus	oesophagus
15	chr9:71992800-72000200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:71992800-72001400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:71993000-72006600	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:71994400-72006800	Weak transcription	Spleen	Spleen
19	chr9:71994800-72000200	Weak transcription	Pancreas	Pancrea
20	chr9:71995000-72000200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr9:71995000-72000600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:71995000-72000800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:71995000-72012600	Weak transcription	Aorta	Aorta
24	chr9:71996000-72000400	Weak transcription	HUVEC	blood vessel
25	chr9:71996200-72000200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:71996200-72000200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:71996200-72000800	Weak transcription	Lung	lung
28	chr9:71996200-72001800	Weak transcription	Left Ventricle	heart
29	chr9:71996600-72000800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:71996600-72002000	Weak transcription	Colon Smooth Muscle	Colon
31	chr9:71996600-72004200	Weak transcription	Right Atrium	heart
32	chr9:71997200-72001800	Weak transcription	Psoas Muscle	Psoas
33	chr9:71997200-72005000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr9:71997200-72006600	Weak transcription	HSMMtube	muscle
35	chr9:71997400-72000400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr9:71997400-72000400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:71997400-72001800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr9:71997400-72002000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:71997400-72007400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:71997400-72009800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:71997600-72000800	Weak transcription	Fetal Heart	heart
42	chr9:71997600-72006200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr9:71997600-72006600	Weak transcription	Fetal Lung	lung
44	chr9:71998200-72005400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
45	chr9:71998400-72000200	Strong transcription	Right Ventricle	heart
46	chr9:71998400-72003600	Strong transcription	Fetal Stomach	stomach
47	chr9:71998600-72000200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:71998600-72000200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr9:71998600-72003000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:71999000-72000200	Weak transcription	Fetal Muscle Leg	muscle

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