Variant report

Variant	rs3824988
Chromosome Location	chr11:57377968-57377969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10750866	0.82[ASN][1000 genomes]
rs10896631	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896632	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896633	1.00[ASW][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap]
rs10896636	0.86[YRI][hapmap]
rs11229063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229067	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229075	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229077	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11229078	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11229080	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11570190	0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap]
rs11570195	0.90[LWK][hapmap]
rs11603020	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605731	1.00[JPT][hapmap]
rs11606677	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11606706	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11607056	0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap]
rs11607122	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11820040	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12804972	1.00[JPT][hapmap]
rs12805841	1.00[JPT][hapmap]
rs1647395	0.82[ASN][1000 genomes]
rs1647405	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2081361	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs28362934	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[YRI][hapmap];0.93[ASN][1000 genomes]
rs28362947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362949	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362950	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847308	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs34052104	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3758918	0.93[ASN][1000 genomes]
rs3758919	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[YRI][hapmap];0.93[ASN][1000 genomes]
rs4926	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs499188	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs55649513	0.82[ASN][1000 genomes]
rs55920079	0.82[ASN][1000 genomes]
rs576859	1.00[JPT][hapmap]
rs7102271	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7117878	0.88[AFR][1000 genomes]
rs7117896	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs731384	1.00[ASW][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.86[AFR][1000 genomes]
rs73480556	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9420	0.82[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3824988	OR8J1	cis	cerebellum	SCAN
rs3824988	OR4D10	cis	parietal	SCAN
rs3824988	YPEL4	cis	multi-tissue	Pritchard
rs3824988	DDB1	cis	cerebellum	SCAN
rs3824988	MS4A7	cis	cerebellum	SCAN
rs3824988	MED19	cis	cerebellum	SCAN
rs3824988	TIMM10	cis	multi-tissue	Pritchard

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57366200-57379000	Weak transcription	Gastric	stomach
2	chr11:57366400-57381800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:57366400-57385800	Weak transcription	Esophagus	oesophagus
4	chr11:57366600-57378800	Weak transcription	Colonic Mucosa	Colon
5	chr11:57366600-57382600	Weak transcription	Brain Substantia Nigra	brain
6	chr11:57366600-57384400	Weak transcription	Pancreas	Pancrea
7	chr11:57366800-57380800	Weak transcription	Brain Anterior Caudate	brain
8	chr11:57366800-57381600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:57366800-57381600	Weak transcription	Osteobl	bone
10	chr11:57366800-57386600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:57366800-57388800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr11:57367000-57387400	Weak transcription	NHDF-Ad	bronchial
13	chr11:57367200-57378800	Weak transcription	Right Ventricle	heart
14	chr11:57367200-57379200	Weak transcription	Fetal Intestine Large	intestine
15	chr11:57367200-57380600	Weak transcription	Fetal Brain Male	brain
16	chr11:57367200-57380600	Weak transcription	Fetal Kidney	kidney
17	chr11:57367400-57381600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:57369000-57385200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr11:57369800-57383400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:57369800-57383400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:57370000-57379000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:57370000-57385200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:57372000-57379200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:57372200-57379000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:57372200-57384600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:57372600-57384400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:57372800-57382600	Weak transcription	Fetal Thymus	thymus
28	chr11:57372800-57383200	Strong transcription	Fetal Muscle Leg	muscle
29	chr11:57372800-57386600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr11:57373000-57383000	Strong transcription	Ovary	ovary
31	chr11:57373000-57383200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:57373200-57384400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:57373200-57384400	Strong transcription	Fetal Lung	lung
34	chr11:57373800-57379000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:57373800-57380600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:57373800-57383400	Weak transcription	NHLF	lung
37	chr11:57373800-57391600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr11:57374000-57379000	Weak transcription	Spleen	Spleen
39	chr11:57374000-57380800	Weak transcription	Small Intestine	intestine
40	chr11:57374000-57386000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr11:57374200-57378800	Weak transcription	Brain Germinal Matrix	brain
42	chr11:57374400-57384200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:57374600-57380600	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:57374600-57381200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr11:57374800-57378800	Weak transcription	Left Ventricle	heart
46	chr11:57375000-57378200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:57375000-57379000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:57375000-57379000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:57375000-57380600	Weak transcription	Fetal Brain Female	brain
50	chr11:57375000-57381000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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