Variant report

Variant	rs3821869
Chromosome Location	chr3:53893840-53893841
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACTR8-1	chr3:53893020-53895603	NONHSAT090006
2	lnc-ACTR8-1	chr3:53893021-53895603	ENSG00000271976.1

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1020082	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1134091	0.84[EUR][1000 genomes]
rs12632292	0.88[EUR][1000 genomes]
rs17053568	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17053590	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs1982171	0.84[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241806	0.84[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2276840	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276843	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276844	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276845	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289203	0.84[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs2304575	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304576	0.84[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs2884631	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3017	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733075	1.00[CEU][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3733079	0.84[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733083	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821868	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41292476	0.83[EUR][1000 genomes]
rs4141606	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45511795	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687594	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs4687753	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687756	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4687758	0.84[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55917919	0.80[EUR][1000 genomes]
rs56743403	0.82[EUR][1000 genomes]
rs57398949	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62253003	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62253004	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6445612	0.84[CEU][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs709324	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7636856	0.85[CEU][hapmap]
rs9840445	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9849951	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9850063	0.88[EUR][1000 genomes]
rs9860367	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9880056	0.84[CEU][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs999514	0.85[CEU][hapmap];0.80[TSI][hapmap]
rs999515	0.85[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	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
7	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
8	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3821869	IL17RB	cis	Cerebellum	GTEx
rs3821869	IL17RB	cis	cerebellum	SCAN
rs3821869	IL17RB	cis	parietal	SCAN
rs3821869	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs3821869	ACTR8	cis	parietal	SCAN
rs3821869	ACTR8	cis	cerebellum	SCAN
rs3821869	ACTR8	Cis_1M	lymphoblastoid	RTeQTL
rs3821869	ACTR8	cis	lymphoblastoid	seeQTL
rs3821869	ACTR8	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53881200-53895000	Weak transcription	A549	lung
2	chr3:53881200-53895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:53884000-53895800	Strong transcription	HepG2	liver
4	chr3:53885000-53901000	Weak transcription	Fetal Heart	heart
5	chr3:53885400-53895200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:53885600-53896600	Weak transcription	Right Ventricle	heart
7	chr3:53886200-53897200	Weak transcription	Colonic Mucosa	Colon
8	chr3:53887800-53898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
10	chr3:53888800-53894400	Weak transcription	Primary T cells from cord blood	blood
11	chr3:53889000-53901400	Weak transcription	Esophagus	oesophagus
12	chr3:53889200-53894400	Strong transcription	Fetal Intestine Small	intestine
13	chr3:53889600-53895200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:53889600-53896000	Strong transcription	Pancreas	Pancrea
15	chr3:53889600-53913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:53889800-53895400	Weak transcription	NHDF-Ad	bronchial
17	chr3:53890000-53895800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:53890000-53904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:53890200-53894400	Weak transcription	Aorta	Aorta
20	chr3:53890200-53895800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:53890400-53894400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:53890400-53895200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:53890400-53898600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:53890400-53898800	Weak transcription	NH-A	brain
25	chr3:53890400-53903600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:53890800-53914600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:53891000-53895000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:53891000-53895800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:53891000-53898000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:53891000-53898000	Weak transcription	Spleen	Spleen
31	chr3:53891000-53914200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:53891000-53914200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr3:53891200-53894200	Weak transcription	Osteobl	bone
34	chr3:53891200-53894800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:53891200-53895000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:53891200-53897800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:53891200-53898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:53891200-53900800	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:53891200-53910800	Strong transcription	Fetal Stomach	stomach
40	chr3:53891400-53898400	Weak transcription	Small Intestine	intestine
41	chr3:53891400-53914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:53891600-53894200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:53891600-53894200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:53891600-53895000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:53891600-53895000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:53891600-53897800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:53891600-53904000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr3:53891800-53895200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr3:53891800-53912800	Strong transcription	Brain Germinal Matrix	brain
50	chr3:53892000-53894000	Strong transcription	Gastric	stomach

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