Variant report

Variant	rs10840096
Chromosome Location	chr11:8643989-8643990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8639960..8642572-chr11:8643233..8645005,2	K562	blood:
2	chr11:8639153..8644664-chr11:8708674..8711558,4	K562	blood:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction
ENSG00000166436	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10734634	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10743083	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10743085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769933	0.92[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10769934	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769937	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11041966	0.84[CHD][hapmap]
rs11042014	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11042026	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042028	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1128559	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs62622852	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7123627	0.82[AFR][1000 genomes]
rs7934978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7950801	0.91[LWK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs9633894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751035	chr11:8431654-8685451	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv896983	chr11:8526643-8682465	ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10840096	LMO1	cis	parietal	SCAN
rs10840096	UBQLN3	cis	parietal	SCAN
rs10840096	APBB1	cis	parietal	SCAN
rs10840096	STK33	cis	cerebellum	SCAN
rs10840096	OR52W1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8626000-8661600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:8626000-8661800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr11:8626200-8653000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:8626600-8648800	Weak transcription	Stomach Mucosa	stomach
5	chr11:8626800-8659600	Weak transcription	Hela-S3	cervix
6	chr11:8630600-8653000	Weak transcription	Osteobl	bone
7	chr11:8630800-8645400	Weak transcription	NHLF	lung
8	chr11:8630800-8645600	Weak transcription	NH-A	brain
9	chr11:8630800-8645800	Weak transcription	NHDF-Ad	bronchial
10	chr11:8631000-8644000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:8632400-8644800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr11:8632600-8644600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr11:8632800-8644200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:8632800-8659000	Weak transcription	Colon Smooth Muscle	Colon
15	chr11:8632800-8663800	Weak transcription	Fetal Kidney	kidney
16	chr11:8634000-8646800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr11:8634200-8647200	Strong transcription	Liver	Liver
18	chr11:8634600-8644000	Weak transcription	Brain Substantia Nigra	brain
19	chr11:8634600-8645600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:8634600-8661600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr11:8634600-8661800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:8634800-8644000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr11:8634800-8657600	Weak transcription	Psoas Muscle	Psoas
24	chr11:8635200-8645400	Weak transcription	HUVEC	blood vessel
25	chr11:8635400-8644000	Weak transcription	HSMM	muscle
26	chr11:8635400-8646800	Weak transcription	Fetal Brain Male	brain
27	chr11:8635400-8647000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:8635400-8661400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr11:8635600-8647000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:8635800-8644600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:8636200-8646400	Weak transcription	Fetal Brain Female	brain
32	chr11:8636200-8646600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:8636200-8661400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:8636600-8657000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr11:8636800-8647000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr11:8636800-8647200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr11:8636800-8647400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:8637000-8647200	Strong transcription	Fetal Intestine Small	intestine
39	chr11:8637000-8661600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr11:8637000-8703200	Weak transcription	Small Intestine	intestine
41	chr11:8637200-8646800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:8637200-8646800	Strong transcription	Placenta	Placenta
43	chr11:8637200-8646800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr11:8637200-8647000	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr11:8637200-8647000	Strong transcription	Lung	lung
46	chr11:8637200-8647200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:8637200-8647200	Strong transcription	Aorta	Aorta
48	chr11:8637200-8647200	Strong transcription	Pancreas	Pancrea
49	chr11:8637200-8647200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr11:8637200-8647200	Strong transcription	Skeletal Muscle Female	skeletal muscle

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