Variant report

Variant	rs3779891
Chromosome Location	chr8:11183505-11183506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10096194	1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10098322	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10099569	0.83[AFR][1000 genomes]
rs10104728	0.83[AFR][1000 genomes]
rs10110557	0.96[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1047950	0.82[CEU][hapmap]
rs10503421	1.00[CEU][hapmap]
rs11250127	0.84[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs11250129	0.88[CEU][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11774673	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11775635	0.89[AFR][1000 genomes]
rs11781375	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11782706	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11784458	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11784544	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11991153	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11994376	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12681987	0.89[CEU][hapmap]
rs13248147	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13250270	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13253016	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13253735	0.91[LWK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13263127	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266233	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13270679	0.87[AFR][1000 genomes]
rs1435273	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1435277	0.82[CEU][hapmap]
rs17741537	1.00[CEU][hapmap];0.91[GIH][hapmap];0.81[EUR][1000 genomes]
rs17797443	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[AFR][1000 genomes]
rs17797894	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1897950	0.81[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs1897951	0.89[AFR][1000 genomes]
rs2060456	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs2060457	0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs2060459	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs2060465	0.81[ASW][hapmap];0.82[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs2164272	0.81[ASW][hapmap];0.82[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs2164273	0.82[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap]
rs2293855	1.00[ASW][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2293856	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2293858	0.81[EUR][1000 genomes]
rs2293859	0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs2293860	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs2572371	0.92[CEU][hapmap]
rs2572452	0.89[CEU][hapmap]
rs2736270	0.82[CEU][hapmap]
rs2736277	0.84[CEU][hapmap]
rs2736280	0.85[CEU][hapmap]
rs2736282	0.89[CEU][hapmap]
rs2736283	0.89[CEU][hapmap]
rs28507159	0.90[AFR][1000 genomes]
rs3174048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34237267	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35392635	0.89[AFR][1000 genomes]
rs35631424	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35687566	0.81[AMR][1000 genomes]
rs35747588	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3808509	0.82[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs3808513	1.00[ASW][hapmap];0.82[CEU][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs3808518	1.00[ASW][hapmap];0.89[GIH][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs4394351	0.81[EUR][1000 genomes]
rs4413734	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs4568582	0.81[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs5029571	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs58283816	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62488721	0.84[EUR][1000 genomes]
rs6601578	1.00[ASW][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs6601580	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6601582	0.85[CEU][hapmap]
rs6985146	0.81[ASW][hapmap];0.82[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6985460	0.81[ASW][hapmap];0.82[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[AFR][1000 genomes]
rs6988922	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6990563	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6991606	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6995404	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6996368	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7003241	0.90[AFR][1000 genomes]
rs7005469	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7008205	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7016671	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7815463	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7815802	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7815804	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7816601	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7816636	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7817658	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7819395	0.96[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7820895	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7828711	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7831346	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7833966	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7834139	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7837036	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7838897	0.96[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7839053	0.96[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1033312	chr8:11126800-11252170	Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv1821756	chr8:11169178-11217587	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv890354	chr8:11176147-11266131	Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv971285	chr8:11181086-11184863	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3779891	C8orf79	cis	parietal	SCAN
rs3779891	TDH	cis	parietal	SCAN
rs3779891	FLJ10661	cis	cerebellum	SCAN
rs3779891	PRSS55	cis	cerebellum	SCAN
rs3779891	TDH	cis	cerebellum	SCAN
rs3779891	MTMR9	Cis_1M	lymphoblastoid	RTeQTL
rs3779891	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs3779891	C8orf48	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11154200-11183800	Strong transcription	Liver	Liver
2	chr8:11155000-11184000	Strong transcription	Dnd41	blood
3	chr8:11162400-11183600	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr8:11162400-11183800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr8:11162400-11184000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr8:11162400-11184000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr8:11162400-11184200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr8:11162600-11184000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr8:11167400-11185200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr8:11167800-11184600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr8:11170600-11185400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr8:11170800-11183800	Strong transcription	Primary hematopoietic stem cells	blood
13	chr8:11171000-11184200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:11171000-11184200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr8:11171600-11191400	Weak transcription	Psoas Muscle	Psoas
16	chr8:11172200-11183600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr8:11174000-11183800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr8:11175400-11185000	Weak transcription	Small Intestine	intestine
19	chr8:11175800-11183800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr8:11176000-11184200	Weak transcription	Right Ventricle	heart
21	chr8:11176000-11184400	Weak transcription	K562	blood
22	chr8:11176000-11185600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:11176000-11187800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr8:11176000-11189000	Weak transcription	Gastric	stomach
25	chr8:11176600-11187000	Weak transcription	Colonic Mucosa	Colon
26	chr8:11177400-11184400	Weak transcription	NHLF	lung
27	chr8:11177800-11184400	Weak transcription	Fetal Brain Male	brain
28	chr8:11177800-11185000	Weak transcription	NH-A	brain
29	chr8:11178200-11186000	Weak transcription	Fetal Intestine Small	intestine
30	chr8:11178200-11186400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr8:11178600-11186800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:11178800-11186200	Weak transcription	Fetal Heart	heart
33	chr8:11179000-11183800	Weak transcription	Pancreas	Pancrea
34	chr8:11179000-11184000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr8:11179000-11185400	Weak transcription	Fetal Lung	lung
36	chr8:11179400-11184000	Weak transcription	Fetal Kidney	kidney
37	chr8:11179400-11187600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr8:11179600-11186200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr8:11179800-11186400	Weak transcription	Brain Germinal Matrix	brain
40	chr8:11179800-11188000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr8:11180400-11184200	Weak transcription	HSMMtube	muscle
42	chr8:11180400-11185000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr8:11180400-11185000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr8:11180600-11184600	Weak transcription	Brain Substantia Nigra	brain
45	chr8:11180600-11185200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr8:11180600-11185400	Weak transcription	Brain Angular Gyrus	brain
47	chr8:11180600-11185800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr8:11180600-11185800	Weak transcription	Fetal Muscle Leg	muscle
49	chr8:11180600-11186000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr8:11180600-11187000	Weak transcription	Lung	lung

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