Variant report

Variant	rs501814
Chromosome Location	chr9:94984150-94984151
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	chr9:94983419..94986395-chr9:94989687..94991728,4	K562	blood:
2	chr9:94982687..94985411-chr9:95009602..95012209,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10125510	0.90[EUR][1000 genomes]
rs1058726	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1058751	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10733744	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10761159	0.90[EUR][1000 genomes]
rs1144933	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1152760	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1152761	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1152762	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1175737	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1175923	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1175929	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1175930	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1175931	0.87[CEU][hapmap]
rs11787696	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11788610	0.82[EUR][1000 genomes]
rs11789578	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11790257	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11791931	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11792542	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11793505	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11794966	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12555097	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2084289	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2295939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2398749	0.84[EUR][1000 genomes]
rs2761680	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs3894058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41280213	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41280215	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs472163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743862	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4743864	0.91[ASN][1000 genomes]
rs4743866	0.87[CEU][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs4743867	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743868	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743871	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744123	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4744124	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4744125	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs556155	0.87[CEU][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs557066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55894730	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56110031	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56308715	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56374228	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6479421	0.90[EUR][1000 genomes]
rs7042199	0.90[EUR][1000 genomes]
rs72748400	0.82[EUR][1000 genomes]
rs72748402	0.82[EUR][1000 genomes]
rs7864453	0.90[EUR][1000 genomes]
rs895639	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409464	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409465	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409466	0.87[CEU][hapmap]
rs9409467	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9409470	0.81[ASN][1000 genomes]
rs9409659	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409660	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409661	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409662	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9409663	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9409665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9409666	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs944949	0.93[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs501814	C9orf79	cis	parietal	SCAN
rs501814	ANKRD19	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94973800-94990400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:94974000-94999000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:94976800-94984800	Weak transcription	Colonic Mucosa	Colon
4	chr9:94982800-94984200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
5	chr9:94982800-94985000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:94982800-94985200	Strong transcription	Primary B cells from cord blood	blood
7	chr9:94982800-94985200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:94982800-94985200	Strong transcription	Brain Germinal Matrix	brain
9	chr9:94982800-94986400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:94982800-94986400	Strong transcription	Brain Hippocampus Middle	brain
11	chr9:94982800-94986600	Strong transcription	Placenta Amnion	Placenta Amnion
12	chr9:94982800-94986800	Strong transcription	Small Intestine	intestine
13	chr9:94982800-94987400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:94982800-94988200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:94982800-94988400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:94982800-94988400	Strong transcription	Aorta	Aorta
17	chr9:94982800-94988400	Strong transcription	Esophagus	oesophagus
18	chr9:94982800-94988400	Strong transcription	Pancreas	Pancrea
19	chr9:94982800-94988600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:94982800-94988600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:94982800-94988600	Strong transcription	Adipose Nuclei	Adipose
22	chr9:94982800-94988600	Strong transcription	Fetal Lung	lung
23	chr9:94982800-94988600	Strong transcription	HMEC	breast
24	chr9:94982800-94988800	Strong transcription	Primary hematopoietic stem cells	blood
25	chr9:94982800-94988800	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:94982800-94988800	Strong transcription	A549	lung
27	chr9:94982800-94988800	Strong transcription	HSMM	muscle
28	chr9:94982800-94989000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:94982800-94989000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr9:94982800-94989000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:94982800-94989000	Strong transcription	Primary T cells from cord blood	blood
32	chr9:94982800-94989000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr9:94982800-94989000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr9:94982800-94989000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr9:94982800-94989000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr9:94982800-94989000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr9:94982800-94989000	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr9:94982800-94989000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr9:94982800-94989000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:94982800-94989000	Strong transcription	Brain Angular Gyrus	brain
41	chr9:94982800-94989000	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr9:94982800-94989000	Strong transcription	Fetal Brain Female	brain
43	chr9:94982800-94989000	Strong transcription	Placenta	Placenta
44	chr9:94982800-94989000	Strong transcription	Gastric	stomach
45	chr9:94982800-94989000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr9:94982800-94989000	Strong transcription	Rectal Smooth Muscle	rectum
47	chr9:94982800-94989000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:94982800-94989000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr9:94982800-94989000	Strong transcription	Dnd41	blood
50	chr9:94982800-94989000	Strong transcription	Hela-S3	cervix

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