Variant report

Variant	rs9878562
Chromosome Location	chr3:53888988-53888989
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	chr3:53888852..53890407-chr3:53890829..53893730,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10440151	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1046677	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1134092	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1157175	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13072145	0.93[ASN][1000 genomes]
rs13315972	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1982172	0.82[EUR][1000 genomes]
rs1992155	1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2083127	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2276846	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3733073	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733081	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816144	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4569647	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687757	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687763	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7624599	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636856	0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[ASN][1000 genomes]
rs893367	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9311516	0.93[ASN][1000 genomes]
rs9311518	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9822471	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9840079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840362	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869505	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9878207	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs999514	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9878562	IL17RB	cis	cerebellum	SCAN
rs9878562	IL17RB	cis	parietal	SCAN
rs9878562	IL17RB	cis	Whole Blood	GTEx
rs9878562	IL17RB	cis	Cerebellum	GTEx
rs9878562	SFMBT1	cis	cerebellum	SCAN
rs9878562	ACTR8	cis	parietal	SCAN
rs9878562	ACTR8	cis	cerebellum	SCAN
rs9878562	SPATA12	cis	cerebellum	SCAN
rs9878562	IL17RB	cis	Artery Tibial	GTEx
rs9878562	CHDH	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53881000-53892600	Weak transcription	Psoas Muscle	Psoas
2	chr3:53881000-53893200	Weak transcription	Ovary	ovary
3	chr3:53881200-53892400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:53881200-53895000	Weak transcription	A549	lung
5	chr3:53881200-53895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:53881400-53889200	Weak transcription	Fetal Intestine Small	intestine
7	chr3:53881400-53891400	Weak transcription	Brain Anterior Caudate	brain
8	chr3:53881400-53892000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:53881400-53892000	Weak transcription	Gastric	stomach
10	chr3:53881400-53892200	Weak transcription	Fetal Intestine Large	intestine
11	chr3:53881400-53892200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:53881400-53892600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:53881400-53892600	Weak transcription	Hela-S3	cervix
14	chr3:53881400-53892800	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:53881400-53893000	Weak transcription	Brain Angular Gyrus	brain
16	chr3:53881400-53893000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:53882400-53891400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:53882600-53892200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:53882800-53892200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:53883000-53891000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:53883200-53889400	Weak transcription	GM12878-XiMat	blood
22	chr3:53884000-53895800	Strong transcription	HepG2	liver
23	chr3:53884400-53892200	Weak transcription	Fetal Brain Female	brain
24	chr3:53884400-53892800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:53885000-53901000	Weak transcription	Fetal Heart	heart
26	chr3:53885200-53892200	Weak transcription	Fetal Lung	lung
27	chr3:53885400-53891200	Weak transcription	Fetal Stomach	stomach
28	chr3:53885400-53892400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:53885400-53892800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:53885400-53895200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:53885600-53892200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:53885600-53892600	Weak transcription	Left Ventricle	heart
33	chr3:53885600-53896600	Weak transcription	Right Ventricle	heart
34	chr3:53886200-53897200	Weak transcription	Colonic Mucosa	Colon
35	chr3:53887600-53891200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:53887600-53892400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:53887800-53889600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:53887800-53889600	Weak transcription	Liver	Liver
39	chr3:53887800-53889600	Weak transcription	Pancreas	Pancrea
40	chr3:53887800-53890600	Weak transcription	Brain Substantia Nigra	brain
41	chr3:53887800-53891000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:53887800-53891200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:53887800-53892800	Weak transcription	Lung	lung
44	chr3:53887800-53898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:53888000-53892400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
47	chr3:53888800-53890800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:53888800-53891800	Weak transcription	Brain Germinal Matrix	brain
49	chr3:53888800-53892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:53888800-53892600	Weak transcription	Fetal Muscle Leg	muscle

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