Variant report

Variant	rs4477456
Chromosome Location	chr11:57197781-57197782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57197604..57200405-chr11:57246413..57248386,2	K562	blood:
2	chr11:57197274..57199985-chr11:57224146..57225779,2	K562	blood:
3	chr11:57196020..57198487-chr11:57226269..57229140,2	K562	blood:
4	chr11:57194860..57196606-chr11:57196687..57198293,2	MCF-7	breast:
5	chr11:57088588..57090285-chr11:57197679..57199918,2	K562	blood:

Variant related genes	Relation type
ENSG00000149115	Chromatin interaction
ENSG00000134802	Chromatin interaction
ENSG00000186907	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11229028	0.98[ASN][1000 genomes]
rs11820985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11822095	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11822910	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11827928	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11828218	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]
rs12422015	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12788236	0.83[ASN][1000 genomes]
rs2250887	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2439448	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581924	0.87[ASN][1000 genomes]
rs2581928	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2584858	0.84[ASN][1000 genomes]
rs2729389	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2869510	0.81[ASN][1000 genomes]
rs35677854	0.81[ASN][1000 genomes]
rs4529894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60961847	0.92[ASN][1000 genomes]
rs61886978	0.96[ASN][1000 genomes]
rs7106223	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7122734	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4477456	SLC43A1	cis	cerebellum	SCAN
rs4477456	DTX4	cis	cerebellum	SCAN
rs4477456	OR8U1	cis	cerebellum	SCAN
rs4477456	TIMM10	cis	cerebellum	SCAN
rs4477456	SLC43A3	cis	cerebellum	SCAN
rs4477456	OR5AR1	cis	parietal	SCAN
rs4477456	OR8U1	cis	parietal	SCAN
rs4477456	OR10Q1	cis	parietal	SCAN
rs4477456	OR5T3	cis	parietal	SCAN
rs4477456	OR5AP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57194600-57198400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:57195000-57198200	Enhancers	Liver	Liver
3	chr11:57195000-57198600	Enhancers	Right Atrium	heart
4	chr11:57195000-57199200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:57195000-57200000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:57195000-57201800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:57195000-57202400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:57195200-57198200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:57195400-57198200	Weak transcription	Gastric	stomach
10	chr11:57195400-57198200	Weak transcription	A549	lung
11	chr11:57195400-57198600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr11:57195400-57198600	Weak transcription	GM12878-XiMat	blood
13	chr11:57195400-57199200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:57195400-57199800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:57195400-57199800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:57195400-57199800	Weak transcription	Fetal Thymus	thymus
17	chr11:57195600-57198200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr11:57195600-57198200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:57195600-57198200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr11:57195600-57198400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr11:57195600-57198400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr11:57195600-57199400	Weak transcription	Brain Anterior Caudate	brain
23	chr11:57195600-57199400	Weak transcription	Spleen	Spleen
24	chr11:57195600-57199600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:57195600-57202400	Weak transcription	Pancreas	Pancrea
26	chr11:57195800-57198800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr11:57195800-57199000	Weak transcription	Brain Hippocampus Middle	brain
28	chr11:57195800-57199400	Weak transcription	Adipose Nuclei	Adipose
29	chr11:57195800-57199600	Weak transcription	Brain Substantia Nigra	brain
30	chr11:57195800-57200200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:57195800-57200200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:57195800-57202000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr11:57195800-57202000	Weak transcription	NHEK	skin
34	chr11:57195800-57202400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr11:57195800-57202400	Weak transcription	Esophagus	oesophagus
36	chr11:57196000-57199400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:57196000-57199400	Weak transcription	Osteobl	bone
38	chr11:57196000-57199600	Weak transcription	HMEC	breast
39	chr11:57196000-57200000	Weak transcription	HSMM	muscle
40	chr11:57196000-57200200	Weak transcription	HSMMtube	muscle
41	chr11:57196000-57200400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:57196000-57201800	Weak transcription	Colon Smooth Muscle	Colon
43	chr11:57196200-57198200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:57196200-57199400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:57196200-57199800	Weak transcription	NHLF	lung
46	chr11:57196600-57198000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:57196600-57199600	Weak transcription	NHDF-Ad	bronchial
48	chr11:57196600-57199800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:57197000-57198400	Enhancers	Right Ventricle	heart
50	chr11:57197000-57203000	Enhancers	HepG2	liver

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