Variant report

Variant	rs3847
Chromosome Location	chr11:58976711-58976712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1048444	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10792228	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10896953	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10896956	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10896958	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11229896	0.84[EUR][1000 genomes]
rs11229898	0.82[EUR][1000 genomes]
rs11229899	0.82[EUR][1000 genomes]
rs12280107	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17153461	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1938593	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1938594	0.86[CHB][hapmap]
rs1945592	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1945593	0.84[EUR][1000 genomes]
rs2000875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2211912	1.00[ASW][hapmap];0.98[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs4938915	0.85[EUR][1000 genomes]
rs4939260	0.96[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4939263	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4939267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4939269	0.80[MEX][hapmap]
rs5023474	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5023475	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61689139	0.84[EUR][1000 genomes]
rs656163	0.89[YRI][hapmap]
rs6591510	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6591515	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6591517	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7109866	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7111287	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7113607	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7121247	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7129035	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7129362	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7931234	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7938115	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3847	CYBASC3	cis	cerebellum	SCAN
rs3847	MPEG1	cis	lymphoblastoid	seeQTL
rs3847	UBE2L6	cis	parietal	SCAN
rs3847	TMX2	cis	cerebellum	SCAN
rs3847	SNORD28	cis	cerebellum	SCAN
rs3847	CYBASC3	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58950000-58978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:58956400-58977400	Weak transcription	Hela-S3	cervix
3	chr11:58964400-58977400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:58965800-58978000	Weak transcription	Left Ventricle	heart
5	chr11:58972000-58977600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
6	chr11:58973400-58978200	Weak transcription	Esophagus	oesophagus
7	chr11:58973400-58983200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:58973600-58977000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:58973600-58977200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:58973600-58982000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:58973800-58977400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:58973800-58979600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:58973800-58984000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:58974200-58976800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:58974400-58977200	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
16	chr11:58974600-58976800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:58974600-58977000	Weak transcription	Fetal Kidney	kidney
18	chr11:58974600-58978600	Weak transcription	Pancreas	Pancrea
19	chr11:58974600-58978800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:58974800-58976800	Flanking Active TSS	GM12878-XiMat	blood
21	chr11:58974800-58977400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:58974800-58977800	Weak transcription	Colonic Mucosa	Colon
23	chr11:58974800-58980200	Weak transcription	Brain Germinal Matrix	brain
24	chr11:58975000-58980400	Weak transcription	Fetal Brain Female	brain
25	chr11:58975200-58976800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:58975200-58976800	Genic enhancers	Fetal Stomach	stomach
27	chr11:58975200-58977000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:58975200-58977800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:58975200-58980000	Weak transcription	Lung	lung
30	chr11:58975400-58980000	Active TSS	Duodenum Mucosa	Duodenum
31	chr11:58975400-58986600	Weak transcription	Gastric	stomach
32	chr11:58975600-58976800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr11:58975600-58977000	Enhancers	Osteobl	bone
34	chr11:58975600-58977400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:58975600-58977400	Enhancers	HSMMtube	muscle
36	chr11:58975600-58977600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr11:58975600-58978200	Enhancers	Fetal Brain Male	brain
38	chr11:58975600-58978200	Weak transcription	Small Intestine	intestine
39	chr11:58975600-58978800	Weak transcription	Brain Substantia Nigra	brain
40	chr11:58975600-58980200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:58975800-58977000	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr11:58975800-58977800	Weak transcription	Fetal Intestine Small	intestine
43	chr11:58975800-58978000	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:58975800-58978400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:58975800-58978400	Weak transcription	Brain Anterior Caudate	brain
46	chr11:58975800-58980000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:58975800-58980400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:58975800-58980400	Active TSS	Fetal Intestine Large	intestine
49	chr11:58975800-58980800	Active TSS	Adipose Nuclei	Adipose
50	chr11:58975800-58981800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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