Variant report

Variant	rs16908001
Chromosome Location	chr11:10609248-10609249
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:10562158..10565041-chr11:10605864..10609739,3	K562	blood:
2	chr11:10601941..10604127-chr11:10608472..10610225,2	K562	blood:
3	chr11:10607679..10609849-chr11:10628348..10630099,2	MCF-7	breast:
4	chr11:10609197..10611359-chr11:10611921..10613725,2	K562	blood:

Variant related genes	Relation type
ENSG00000110315	Chromatin interaction
ENSG00000177112	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1035691	1.00[JPT][hapmap]
rs10840457	1.00[JPT][hapmap]
rs11042902	1.00[JPT][hapmap]
rs11603178	1.00[JPT][hapmap]
rs1364738	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1364739	1.00[ASN][1000 genomes]
rs1462940	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs16927077	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs17318955	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17403175	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17403439	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17403460	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17403795	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17403942	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17403977	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1863243	1.00[JPT][hapmap]
rs1863244	1.00[JPT][hapmap]
rs1979367	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2098839	1.00[JPT][hapmap]
rs4025	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41464450	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4442541	1.00[JPT][hapmap]
rs4909945	1.00[JPT][hapmap]
rs4910160	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4910165	1.00[JPT][hapmap]
rs6484336	1.00[CHB][hapmap]
rs7940646	1.00[JPT][hapmap]
rs7949992	1.00[ASN][1000 genomes]
rs7950829	1.00[ASN][1000 genomes]
rs7952446	1.00[ASN][1000 genomes]
rs881869	1.00[JPT][hapmap]
rs903822	1.00[JPT][hapmap]
rs903823	1.00[JPT][hapmap]

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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16908001	DKK3	cis	cerebellum	SCAN
rs16908001	AMPD3	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10580600-10609800	Weak transcription	Thymus	Thymus
2	chr11:10586400-10620400	Weak transcription	Brain Anterior Caudate	brain
3	chr11:10590600-10611200	Weak transcription	Pancreas	Pancrea
4	chr11:10592400-10622600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:10595000-10629600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:10595000-10632800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr11:10595400-10615400	Weak transcription	Brain Angular Gyrus	brain
8	chr11:10597200-10625800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr11:10601200-10611800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr11:10602800-10611400	Enhancers	K562	blood
11	chr11:10603000-10609600	Weak transcription	Brain Substantia Nigra	brain
12	chr11:10603200-10613200	Weak transcription	Fetal Intestine Large	intestine
13	chr11:10603600-10614800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:10603600-10614800	Weak transcription	Fetal Intestine Small	intestine
15	chr11:10603600-10621800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:10605200-10609400	Enhancers	Ovary	ovary
17	chr11:10605200-10620400	Weak transcription	Fetal Thymus	thymus
18	chr11:10605600-10609600	Weak transcription	Primary B cells from cord blood	blood
19	chr11:10605800-10610200	Weak transcription	Colonic Mucosa	Colon
20	chr11:10605800-10611200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr11:10605800-10611400	Weak transcription	Fetal Muscle Leg	muscle
22	chr11:10605800-10613400	Weak transcription	Psoas Muscle	Psoas
23	chr11:10605800-10614000	Weak transcription	Gastric	stomach
24	chr11:10605800-10622200	Weak transcription	Spleen	Spleen
25	chr11:10606000-10609800	Weak transcription	Aorta	Aorta
26	chr11:10606000-10610400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr11:10606000-10612600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr11:10606000-10620400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr11:10607000-10610400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr11:10607000-10611400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:10607000-10612200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr11:10607000-10613600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:10607200-10610600	Strong transcription	Fetal Stomach	stomach
34	chr11:10607200-10612200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr11:10607200-10616800	Enhancers	Placenta	Placenta
36	chr11:10607400-10626000	Weak transcription	Fetal Lung	lung
37	chr11:10607800-10609600	Enhancers	Osteobl	bone
38	chr11:10608000-10609400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:10608000-10611400	Enhancers	NHEK	skin
40	chr11:10608200-10609400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:10608200-10609400	Enhancers	Left Ventricle	heart
42	chr11:10608200-10609400	Enhancers	HSMMtube	muscle
43	chr11:10608200-10609600	Strong transcription	Brain Hippocampus Middle	brain
44	chr11:10608200-10609600	Enhancers	NHDF-Ad	bronchial
45	chr11:10608200-10609600	Enhancers	NHLF	lung
46	chr11:10608400-10609600	Enhancers	Esophagus	oesophagus
47	chr11:10608400-10609600	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr11:10608400-10611400	Weak transcription	Lung	lung
49	chr11:10608400-10616000	Enhancers	Placenta Amnion	Placenta Amnion
50	chr11:10608600-10609400	Enhancers	Muscle Satellite Cultured Cells	--

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