Variant report

Variant	rs2279518
Chromosome Location	chr11:76573016-76573017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:76494290..76496487-chr11:76570623..76573983,3	K562	blood:
2	chr11:76494634..76496487-chr11:76571954..76573983,2	K562	blood:
3	chr11:76518255..76520298-chr11:76572077..76574099,2	MCF-7	breast:
4	chr11:76572033..76573860-chr11:76603838..76606079,2	MCF-7	breast:
5	chr11:76572318..76575156-chr11:76600227..76602502,2	K562	blood:
6	chr11:76493101..76495858-chr11:76570734..76573156,2	MCF-7	breast:
7	chr11:76478547..76482353-chr11:76570414..76574348,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182704	Chromatin interaction
ENSG00000255100	Chromatin interaction
ENSG00000254632	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10899293	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236997	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237030	0.80[EUR][1000 genomes]
rs11602065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11606034	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11606467	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12223477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1225138	0.82[GIH][hapmap]
rs1945084	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1945085	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2048954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2187499	0.82[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2372387	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3740766	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3740768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs4016126	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4945128	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs55743360	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55798841	0.80[EUR][1000 genomes]
rs56129156	0.80[EUR][1000 genomes]
rs56789915	0.80[EUR][1000 genomes]
rs61895512	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61895513	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61900090	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7115729	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518920	chr11:76573016-76637651	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2279518	ALG8	cis	parietal	SCAN
rs2279518	FCHSD2	cis	cerebellum	SCAN
rs2279518	ACER3	cis	parietal	SCAN
rs2279518	KLHL35	cis	cerebellum	SCAN
rs2279518	SNORD15B	cis	parietal	SCAN
rs2279518	GDPD5	cis	parietal	SCAN
rs2279518	ACER3	cis	lymphoblastoid	seeQTL
rs2279518	CAPN5	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76571400-76573400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr11:76571600-76573400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr11:76572000-76573200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:76572000-76573200	Flanking Active TSS	Placenta	Placenta
5	chr11:76572200-76573200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr11:76572200-76573200	Flanking Active TSS	Dnd41	blood
7	chr11:76572400-76573200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:76572400-76573200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:76572400-76573200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
10	chr11:76572400-76573200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr11:76572400-76573200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:76572400-76573200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr11:76572400-76573200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:76572400-76573200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:76572400-76573200	Flanking Active TSS	Colonic Mucosa	Colon
16	chr11:76572400-76573200	Flanking Active TSS	Fetal Intestine Small	intestine
17	chr11:76572400-76573200	Flanking Active TSS	Fetal Lung	lung
18	chr11:76572400-76573200	Flanking Active TSS	Right Ventricle	heart
19	chr11:76572400-76573200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr11:76572400-76573200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr11:76572400-76573200	Flanking Active TSS	Stomach Mucosa	stomach
22	chr11:76572400-76573200	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr11:76572400-76573200	Flanking Active TSS	GM12878-XiMat	blood
24	chr11:76572400-76573200	Flanking Active TSS	HUVEC	blood vessel
25	chr11:76572400-76573400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:76572400-76573400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr11:76572400-76573400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:76572400-76573400	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr11:76572400-76573400	Flanking Active TSS	Brain Cingulate Gyrus	brain
30	chr11:76572400-76573400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr11:76572400-76573400	Flanking Active TSS	K562	blood
32	chr11:76572400-76573600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:76572400-76573600	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr11:76572400-76574000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:76572600-76573200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr11:76572600-76573200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
37	chr11:76572600-76573200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:76572600-76573200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:76572600-76573200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr11:76572600-76573200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
41	chr11:76572600-76573200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:76572600-76573200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr11:76572600-76573200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:76572600-76573200	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr11:76572600-76573200	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr11:76572600-76573200	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr11:76572600-76573200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr11:76572600-76573200	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr11:76572600-76573200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr11:76572600-76573200	Flanking Active TSS	Fetal Kidney	kidney

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