Variant report

Variant	rs4513721
Chromosome Location	chr5:95452324-95452325
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10056771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10079268	0.86[EUR][1000 genomes]
rs10085034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11740207	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949461	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11951463	0.81[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap]
rs11956456	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11960219	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13155375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13172783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13172805	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13186419	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2067498	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4077350	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4128178	0.81[CEU][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4270717	0.83[EUR][1000 genomes]
rs4367316	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4416625	0.81[CEU][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4479864	0.86[EUR][1000 genomes]
rs4869256	0.81[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs4869258	0.83[EUR][1000 genomes]
rs4869259	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869260	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869264	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4869266	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4998057	0.83[EUR][1000 genomes]
rs6556899	0.83[EUR][1000 genomes]
rs66683317	0.83[EUR][1000 genomes]
rs6866723	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs6873504	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6879658	0.86[EUR][1000 genomes]
rs6879847	0.86[EUR][1000 genomes]
rs6884999	0.83[EUR][1000 genomes]
rs6886983	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6889697	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6894768	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6895121	0.85[EUR][1000 genomes]
rs6895146	0.81[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs7341111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7700425	0.85[EUR][1000 genomes]
rs7702346	0.94[EUR][1000 genomes]
rs7702646	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7710337	0.85[EUR][1000 genomes]
rs7715650	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7734224	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7734985	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9314165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv823146	chr5:95300912-95453557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	esv2757121	chr5:95304236-95539536	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	esv34203	chr5:95310985-95452324	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
7	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4513721	SPATA9	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95430600-95454400	Weak transcription	Aorta	Aorta
2	chr5:95445400-95455800	Weak transcription	Gastric	stomach
3	chr5:95447200-95454000	Weak transcription	Pancreas	Pancrea
4	chr5:95448000-95453600	Enhancers	Liver	Liver
5	chr5:95448600-95453000	Enhancers	HepG2	liver
6	chr5:95449200-95454600	Enhancers	Fetal Intestine Small	intestine
7	chr5:95449600-95452600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:95450200-95453000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:95450200-95453400	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:95450600-95452600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:95450600-95452800	Enhancers	Fetal Intestine Large	intestine
12	chr5:95450600-95453400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:95450600-95453800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:95450600-95453800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:95450600-95454000	Weak transcription	HSMMtube	muscle
16	chr5:95450800-95453800	Weak transcription	NHDF-Ad	bronchial
17	chr5:95450800-95454200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr5:95451000-95454000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:95451000-95454400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:95451200-95461000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:95451400-95452600	Weak transcription	Stomach Mucosa	stomach
22	chr5:95451400-95453600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:95451400-95453600	Weak transcription	A549	lung
24	chr5:95451400-95454000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:95451400-95454400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:95451400-95460800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:95451400-95461200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:95451600-95453600	Weak transcription	HMEC	breast
29	chr5:95451600-95453600	Weak transcription	NHEK	skin
30	chr5:95452000-95455600	Weak transcription	HUVEC	blood vessel
31	chr5:95452200-95455400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:95452200-95456000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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