Variant report

Variant	rs301878
Chromosome Location	chr5:37097138-37097139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10061157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10073054	0.91[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10079030	0.80[EUR][1000 genomes]
rs10512664	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10941321	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12658479	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs13166974	0.81[ASN][1000 genomes]
rs13169211	0.87[ASN][1000 genomes]
rs13171526	0.85[ASN][1000 genomes]
rs13184464	0.94[JPT][hapmap]
rs159755	0.80[CEU][hapmap]
rs16903531	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2098713	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs216385	0.80[EUR][1000 genomes]
rs301863	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs301867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs301869	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs301872	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs301873	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs301874	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs301905	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs301906	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs301908	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs301909	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6451313	0.88[EUR][1000 genomes]
rs6859950	0.84[YRI][hapmap]
rs6860727	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6868809	0.84[YRI][hapmap]
rs6886108	0.81[EUR][1000 genomes]
rs6887958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7711452	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7712558	0.84[YRI][hapmap]
rs7715883	0.83[EUR][1000 genomes]
rs7729404	0.84[EUR][1000 genomes]
rs7735138	0.84[EUR][1000 genomes]
rs9632396	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1024051	chr5:36899712-37303001	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv537725	chr5:36899712-37303001	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv917880	chr5:36948778-37115342	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	esv1802391	chr5:36958598-37242600	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv597822	chr5:36997953-37147152	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv534064	chr5:37054962-37586210	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv964844	chr5:37080836-37107123	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv881511	chr5:37088627-37552852	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs301878	C5orf42	cis	cerebellum	SCAN
rs301878	GDNF	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37061200-37103400	Weak transcription	Fetal Kidney	kidney
2	chr5:37064200-37105000	Weak transcription	Fetal Brain Male	brain
3	chr5:37064600-37104000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:37065000-37097400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:37065000-37099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:37065000-37107600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:37065200-37103400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:37065600-37102400	Weak transcription	Placenta	Placenta
9	chr5:37067000-37111400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:37072600-37097400	Weak transcription	Brain Angular Gyrus	brain
11	chr5:37072600-37103600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:37073400-37103600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:37078800-37097600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:37078800-37105000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:37080000-37098600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:37080000-37103800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:37080200-37112000	Weak transcription	Fetal Heart	heart
18	chr5:37080600-37102200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:37080800-37097400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:37082000-37109000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:37082800-37169200	Weak transcription	Spleen	Spleen
22	chr5:37085400-37103200	Weak transcription	Thymus	Thymus
23	chr5:37085600-37099600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:37085600-37103400	Weak transcription	Left Ventricle	heart
25	chr5:37087000-37104400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:37087000-37105200	Weak transcription	Lung	lung
27	chr5:37087000-37107000	Weak transcription	Pancreas	Pancrea
28	chr5:37087200-37097400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:37087200-37106800	Weak transcription	Hela-S3	cervix
30	chr5:37087200-37113600	Weak transcription	NH-A	brain
31	chr5:37087400-37098200	Weak transcription	Aorta	Aorta
32	chr5:37087400-37102600	Weak transcription	HSMM	muscle
33	chr5:37087400-37103200	Weak transcription	Dnd41	blood
34	chr5:37087600-37103200	Weak transcription	Fetal Thymus	thymus
35	chr5:37087600-37105000	Weak transcription	Osteobl	bone
36	chr5:37088800-37103400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:37091200-37102200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:37092600-37104600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:37092600-37104800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:37092800-37097400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:37092800-37104400	Weak transcription	Ovary	ovary
42	chr5:37093000-37103200	Weak transcription	HSMMtube	muscle
43	chr5:37094200-37097400	Weak transcription	Liver	Liver
44	chr5:37094200-37106400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:37096000-37097200	Weak transcription	Fetal Lung	lung
46	chr5:37096400-37097400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:37096400-37103400	Weak transcription	NHDF-Ad	bronchial

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