Variant report

Variant	rs11828218
Chromosome Location	chr11:57196223-57196224
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr11:57196213-57196407	K562	blood:	n/a	n/a
2	TBL1XR1	chr11:57196132-57196276	K562	blood:	n/a	n/a
3	CCNT2	chr11:57196172-57196399	K562	blood:	n/a	n/a
4	UBTF	chr11:57196147-57196484	K562	blood:	n/a	n/a
5	EP300	chr11:57196100-57196482	K562	blood:	n/a	chr11:57196190-57196204
6	UBTF	chr11:57196195-57196402	K562	blood:	n/a	n/a
7	TAL1	chr11:57196146-57196474	K562	blood:	n/a	n/a
8	RCOR1	chr11:57196136-57196491	K562	blood:	n/a	n/a
9	BHLHE40	chr11:57196132-57196484	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57194854..57196805-chr11:57435548..57437119,2	K562	blood:
2	chr11:57196020..57198487-chr11:57226269..57229140,2	K562	blood:
3	chr11:57195352..57196928-chr11:57214427..57216091,2	K562	blood:
4	chr11:57094351..57096693-chr11:57193203..57197242,3	K562	blood:

No data

Variant related genes	Relation type
SLC43A3	TF binding region
ENSG00000254979	TF binding region
ENSG00000186907	Chromatin interaction
ENSG00000156599	Chromatin interaction
ENSG00000238692	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11229028	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11820985	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11822095	1.00[ASN][1000 genomes]
rs11822910	0.98[ASN][1000 genomes]
rs11827928	0.98[ASN][1000 genomes]
rs12422015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12788236	0.81[ASN][1000 genomes]
rs2250887	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2439448	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467333	0.81[EUR][1000 genomes]
rs2511982	0.85[EUR][1000 genomes]
rs2581924	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2581927	0.87[EUR][1000 genomes]
rs2581928	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2584858	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2729389	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2729392	0.87[EUR][1000 genomes]
rs4477456	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4529894	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs60961847	0.91[ASN][1000 genomes]
rs61886978	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7106223	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7122734	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7943531	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11828218	TIMM10	cis	cerebellum	SCAN
rs11828218	OR5AR1	cis	parietal	SCAN
rs11828218	OR5AP2	cis	parietal	SCAN
rs11828218	TIMM10	cis	parietal	SCAN
rs11828218	OR5T3	cis	parietal	SCAN
rs11828218	OR8U1	cis	cerebellum	SCAN
rs11828218	SLC43A1	cis	cerebellum	SCAN
rs11828218	SLC43A3	cis	cerebellum	SCAN
rs11828218	DTX4	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57194400-57197000	Weak transcription	HepG2	liver
2	chr11:57194600-57198400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:57195000-57196400	Enhancers	Fetal Muscle Leg	muscle
4	chr11:57195000-57196600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:57195000-57198200	Enhancers	Liver	Liver
6	chr11:57195000-57198600	Enhancers	Right Atrium	heart
7	chr11:57195000-57199200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:57195000-57200000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:57195000-57201800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr11:57195000-57202400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr11:57195200-57197200	Enhancers	K562	blood
12	chr11:57195200-57198200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:57195400-57198200	Weak transcription	Gastric	stomach
14	chr11:57195400-57198200	Weak transcription	A549	lung
15	chr11:57195400-57198600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:57195400-57198600	Weak transcription	GM12878-XiMat	blood
17	chr11:57195400-57199200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:57195400-57199800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:57195400-57199800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:57195400-57199800	Weak transcription	Fetal Thymus	thymus
21	chr11:57195600-57196600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:57195600-57196600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:57195600-57196600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr11:57195600-57197000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:57195600-57197000	Weak transcription	Right Ventricle	heart
26	chr11:57195600-57197200	Weak transcription	Stomach Mucosa	stomach
27	chr11:57195600-57197600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:57195600-57198200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:57195600-57198200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:57195600-57198200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr11:57195600-57198400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr11:57195600-57198400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr11:57195600-57199400	Weak transcription	Brain Anterior Caudate	brain
34	chr11:57195600-57199400	Weak transcription	Spleen	Spleen
35	chr11:57195600-57199600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:57195600-57202400	Weak transcription	Pancreas	Pancrea
37	chr11:57195800-57196600	Enhancers	NHDF-Ad	bronchial
38	chr11:57195800-57196800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr11:57195800-57196800	Weak transcription	Aorta	Aorta
40	chr11:57195800-57196800	Weak transcription	Left Ventricle	heart
41	chr11:57195800-57197000	Weak transcription	Lung	lung
42	chr11:57195800-57198800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr11:57195800-57199000	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:57195800-57199400	Weak transcription	Adipose Nuclei	Adipose
45	chr11:57195800-57199600	Weak transcription	Brain Substantia Nigra	brain
46	chr11:57195800-57200200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:57195800-57200200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:57195800-57202000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:57195800-57202000	Weak transcription	NHEK	skin
50	chr11:57195800-57202400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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