Variant report

Variant	rs1004385
Chromosome Location	chr5:111678637-111678638
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	chr5:111678130..111679875-chr5:111682477..111684112,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1004383	0.98[ASN][1000 genomes]
rs10052915	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1019743	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs1019744	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs11743178	0.87[CHB][hapmap]
rs12519600	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs1464764	0.81[CHB][hapmap]
rs1474360	0.94[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs1524426	0.81[CHB][hapmap]
rs1962305	0.83[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1975017	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2042884	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2056585	0.83[CHB][hapmap]
rs2140625	0.89[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2140626	0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2416283	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2416284	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2839826	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs366217	0.91[ASN][1000 genomes]
rs366951	0.91[ASN][1000 genomes]
rs367807	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs368032	0.89[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs370640	0.91[ASN][1000 genomes]
rs373303	0.94[ASN][1000 genomes]
rs373583	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs376395	0.96[ASN][1000 genomes]
rs378791	0.86[ASN][1000 genomes]
rs382482	0.91[ASN][1000 genomes]
rs387117	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs388091	0.92[ASN][1000 genomes]
rs393096	0.87[ASN][1000 genomes]
rs406359	0.89[ASN][1000 genomes]
rs406444	0.96[ASN][1000 genomes]
rs408076	0.83[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs408127	0.89[ASN][1000 genomes]
rs424998	0.96[ASN][1000 genomes]
rs429580	0.93[ASN][1000 genomes]
rs440759	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs441563	0.94[ASN][1000 genomes]
rs442777	0.92[ASN][1000 genomes]
rs442947	0.91[ASN][1000 genomes]
rs443024	0.97[ASN][1000 genomes]
rs447144	0.96[ASN][1000 genomes]
rs4479888	0.85[ASN][1000 genomes]
rs454794	0.95[ASN][1000 genomes]
rs4958040	0.98[ASN][1000 genomes]
rs4958043	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6594591	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6861186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6872155	0.88[ASN][1000 genomes]
rs6877695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706772	0.81[CHB][hapmap]
rs7711318	0.98[ASN][1000 genomes]
rs7720180	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7720546	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7731169	0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs821733	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs821734	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs821735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs821745	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs821747	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs987764	0.98[ASN][1000 genomes]
rs987765	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1021530	chr5:111626266-111683317	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1028181	chr5:111628901-111683317	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv882714	chr5:111655382-111807579	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv462386	chr5:111667572-111699317	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv599372	chr5:111667572-111699317	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1004385	PJA2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111637400-111684600	Weak transcription	Aorta	Aorta
2	chr5:111669800-111683600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:111675000-111682800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:111675600-111687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:111676200-111689000	Weak transcription	Lung	lung
6	chr5:111677800-111678800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:111677800-111678800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr5:111678000-111678800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:111678000-111679000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:111678000-111679200	Enhancers	Brain Hippocampus Middle	brain
11	chr5:111678200-111678800	Enhancers	Right Atrium	heart
12	chr5:111678200-111679400	Enhancers	Left Ventricle	heart
13	chr5:111678400-111683600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:111678400-111684600	Weak transcription	Right Ventricle	heart
15	chr5:111678400-111689000	Weak transcription	Gastric	stomach
16	chr5:111678600-111679400	Enhancers	Fetal Heart	heart
17	chr5:111678600-111682600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:111678600-111683400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:111678600-111683600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:111678600-111683600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:111678600-111683800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:111678600-111695600	Weak transcription	Pancreas	Pancrea

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