Variant report

Variant	rs6873504
Chromosome Location	chr5:95431343-95431344
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

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];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11740207	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11949461	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11951463	0.81[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap]
rs11956456	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960219	0.97[EUR][1000 genomes];0.84[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];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13172805	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13186419	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2067498	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4077350	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4128178	0.81[CEU][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4270717	0.84[EUR][1000 genomes]
rs4367316	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[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]
rs4513721	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869260	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869264	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4869266	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4998057	0.84[EUR][1000 genomes]
rs6556899	0.84[EUR][1000 genomes]
rs66683317	0.84[EUR][1000 genomes]
rs6866723	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs6879658	0.86[EUR][1000 genomes]
rs6879847	0.86[EUR][1000 genomes]
rs6884999	0.84[EUR][1000 genomes]
rs6886983	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889697	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894768	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7700425	0.85[EUR][1000 genomes]
rs7702346	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7702646	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7710337	0.85[EUR][1000 genomes]
rs7715650	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7734224	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7734985	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9314164	0.80[EUR][1000 genomes]
rs9314165	0.95[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	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
rs6873504	SPATA9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95419200-95437400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:95426200-95431800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:95426600-95432000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:95426600-95432200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:95427800-95432800	Enhancers	NHEK	skin
6	chr5:95428400-95432400	Enhancers	Hela-S3	cervix
7	chr5:95428600-95432600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:95428600-95432600	Enhancers	HMEC	breast
9	chr5:95428800-95432000	Enhancers	Stomach Mucosa	stomach
10	chr5:95428800-95432200	Enhancers	HepG2	liver
11	chr5:95428800-95432600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:95429000-95431800	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr5:95429000-95433000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:95429000-95433200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:95429200-95431400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr5:95430600-95431800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:95430600-95431800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:95430600-95454400	Weak transcription	Aorta	Aorta
19	chr5:95430800-95431400	Enhancers	Esophagus	oesophagus
20	chr5:95430800-95431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:95430800-95432000	Weak transcription	NHLF	lung
22	chr5:95430800-95432200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:95431000-95431800	Weak transcription	HSMM	muscle
24	chr5:95431000-95432000	Weak transcription	HSMMtube	muscle
25	chr5:95431000-95432200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:95431000-95432200	Weak transcription	Osteobl	bone
27	chr5:95431000-95437600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:95431200-95431600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:95431200-95431600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:95431200-95431600	Weak transcription	NHDF-Ad	bronchial
31	chr5:95431200-95432200	Weak transcription	A549	lung
32	chr5:95431200-95437200	Weak transcription	Pancreas	Pancrea

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