Variant report

Variant	rs228606
Chromosome Location	chr11:108087847-108087848
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:108087405..108089573-chr11:108637828..108639392,2	K562	blood:
2	chr11:108087467..108089290-chr11:108094676..108097621,3	MCF-7	breast:
3	chr11:108069760..108073247-chr11:108087565..108091000,4	K562	blood:

Variant related genes	Relation type
ENSG00000178105	Chromatin interaction
ENSG00000149311	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10789659	0.85[CHB][hapmap]
rs10890813	0.80[JPT][hapmap]
rs10890819	0.85[JPT][hapmap]
rs10890834	0.85[CHB][hapmap]
rs11212515	0.85[JPT][hapmap]
rs11212538	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs11212542	0.81[ASN][1000 genomes]
rs11212546	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11212551	0.95[CHB][hapmap]
rs11212617	0.80[MEX][hapmap]
rs113995	0.90[CHB][hapmap]
rs11605442	0.94[CHB][hapmap]
rs12787445	0.91[CHB][hapmap]
rs1607476	0.91[CHB][hapmap]
rs170548	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs172894	0.86[CHB][hapmap]
rs172896	0.90[CHB][hapmap]
rs183459	0.91[CHB][hapmap]
rs183460	0.95[CHB][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs1850730	0.95[CHB][hapmap]
rs186595	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs189037	0.88[ASN][1000 genomes]
rs2056267	0.89[CHB][hapmap]
rs2083707	0.91[CHB][hapmap]
rs227040	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs227041	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs227055	0.86[CHB][hapmap]
rs227058	0.86[CHB][hapmap]
rs227060	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs227061	0.90[CHB][hapmap]
rs227062	0.85[CHB][hapmap]
rs227064	0.86[CHB][hapmap]
rs227068	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs227069	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs227070	0.86[CHB][hapmap]
rs227072	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs227073	0.90[CHB][hapmap]
rs227074	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs227075	0.86[CHB][hapmap]
rs227077	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs227087	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs227092	0.86[CHB][hapmap]
rs228589	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs228590	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs228591	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs228592	0.86[CHB][hapmap]
rs228593	0.81[GIH][hapmap]
rs228595	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs228596	0.80[ASN][1000 genomes]
rs228599	0.86[CHB][hapmap]
rs228608	0.82[ASN][1000 genomes]
rs2356801	0.80[MEX][hapmap]
rs373759	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs3741056	0.90[JPT][hapmap]
rs374443	0.86[CHB][hapmap]
rs3781868	0.95[CHB][hapmap]
rs3781869	0.81[ASN][1000 genomes]
rs419716	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs425538	0.86[CHB][hapmap]
rs4585	0.82[CHB][hapmap]
rs4623864	0.95[CHB][hapmap];0.80[MEX][hapmap]
rs4753833	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4754305	0.95[CHB][hapmap];0.80[MEX][hapmap]
rs4987876	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs573890	0.90[CHB][hapmap]
rs595747	0.82[CHB][hapmap]
rs597788	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs599164	0.81[CHB][hapmap]
rs599406	0.90[CHB][hapmap]
rs599558	0.90[CHB][hapmap]
rs600931	0.86[CHB][hapmap]
rs609557	0.95[CHB][hapmap];0.80[MEX][hapmap];0.82[ASN][1000 genomes]
rs609655	0.86[CHB][hapmap]
rs611646	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs620613	0.90[CHB][hapmap]
rs623860	0.82[CHB][hapmap]
rs627418	0.86[CHB][hapmap]
rs641605	0.90[CHB][hapmap]
rs651030	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs652311	0.90[CHB][hapmap];0.80[MEX][hapmap]
rs652541	0.86[CHB][hapmap]
rs6589007	0.95[CHB][hapmap]
rs662218	0.86[CHB][hapmap]
rs662578	0.90[CHB][hapmap]
rs664143	0.86[CHB][hapmap]
rs672655	0.95[CHB][hapmap];0.80[MEX][hapmap]
rs673281	0.86[CHB][hapmap]
rs694376	0.86[CHB][hapmap]
rs7114794	0.90[JPT][hapmap]
rs7118967	0.90[CHB][hapmap]
rs7129527	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7931930	0.91[CHB][hapmap];0.80[MEX][hapmap]
rs7932972	0.86[ASN][1000 genomes]
rs920679	0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]

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	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv898383	chr11:108068954-108251211	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs228606	AVIL	trans	parietal	SCAN
rs228606	NPAT	cis	cerebellum	SCAN
rs228606	ACAT1	cis	cerebellum	SCAN
rs228606	KDELC2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108062600-108090800	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:108070600-108089800	Weak transcription	Psoas Muscle	Psoas
3	chr11:108071000-108091600	Weak transcription	Right Atrium	heart
4	chr11:108071400-108092400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:108074400-108090800	Weak transcription	Small Intestine	intestine
6	chr11:108077800-108089200	Weak transcription	HMEC	breast
7	chr11:108078000-108090400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:108078000-108090600	Weak transcription	Fetal Heart	heart
9	chr11:108078200-108089000	Weak transcription	Osteobl	bone
10	chr11:108078200-108089400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:108078200-108089400	Weak transcription	NHDF-Ad	bronchial
12	chr11:108078400-108091800	Weak transcription	HSMMtube	muscle
13	chr11:108078600-108089800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:108078600-108089800	Weak transcription	Pancreas	Pancrea
15	chr11:108078600-108090600	Weak transcription	Aorta	Aorta
16	chr11:108078600-108090800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:108078600-108090800	Weak transcription	Brain Substantia Nigra	brain
18	chr11:108078600-108091600	Weak transcription	Right Ventricle	heart
19	chr11:108078600-108091800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:108078600-108091800	Weak transcription	Lung	lung
21	chr11:108078600-108092200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:108078600-108092200	Weak transcription	Esophagus	oesophagus
23	chr11:108078800-108089800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr11:108078800-108091400	Weak transcription	Adipose Nuclei	Adipose
25	chr11:108078800-108092200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:108079000-108089200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:108079000-108089800	Weak transcription	Hela-S3	cervix
28	chr11:108079000-108090800	Weak transcription	Brain Anterior Caudate	brain
29	chr11:108079000-108091000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:108079200-108089400	Weak transcription	Brain Hippocampus Middle	brain
31	chr11:108079200-108089800	Weak transcription	Gastric	stomach
32	chr11:108079200-108090400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr11:108079200-108090600	Weak transcription	NHLF	lung
34	chr11:108079200-108091400	Weak transcription	NH-A	brain
35	chr11:108079200-108091800	Weak transcription	Brain Angular Gyrus	brain
36	chr11:108079200-108091800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr11:108079600-108090000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:108079600-108091800	Weak transcription	Colonic Mucosa	Colon
39	chr11:108081400-108089800	Weak transcription	Fetal Brain Male	brain
40	chr11:108081400-108091800	Weak transcription	HSMM	muscle
41	chr11:108081600-108091400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr11:108081600-108091600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr11:108081800-108090600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr11:108081800-108091000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr11:108081800-108091600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr11:108081800-108091600	Weak transcription	A549	lung
47	chr11:108081800-108092200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr11:108082000-108091600	Weak transcription	Placenta	Placenta
49	chr11:108082200-108089400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:108082200-108091800	Weak transcription	Ovary	ovary

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