Variant report

Variant	rs9990216
Chromosome Location	chr3:112074331-112074332
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10804500	0.81[CHB][hapmap]
rs1131199	0.81[CEU][hapmap]
rs12106967	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1317243	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs2895395	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs4355254	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs4682103	0.81[CEU][hapmap]
rs57661530	0.92[ASN][1000 genomes]
rs62264124	0.88[ASN][1000 genomes]
rs72952411	0.92[ASN][1000 genomes]
rs7639471	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[ASN][1000 genomes]
rs7639794	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs9834347	0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs9837466	0.81[CEU][hapmap]
rs9863371	0.81[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs9868582	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9990215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9990216	ZNF80	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112052800-112076200	Weak transcription	Right Ventricle	heart
2	chr3:112053200-112076400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:112054800-112076800	Weak transcription	Lung	lung
4	chr3:112054800-112083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:112055600-112080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:112055800-112076400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:112056600-112076400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:112059600-112075000	Strong transcription	Fetal Thymus	thymus
9	chr3:112061200-112083000	Weak transcription	Colonic Mucosa	Colon
10	chr3:112061400-112076000	Strong transcription	Primary hematopoietic stem cells	blood
11	chr3:112062400-112083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:112062600-112076600	Strong transcription	Primary B cells from cord blood	blood
13	chr3:112062800-112074600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:112064000-112076800	Weak transcription	Left Ventricle	heart
15	chr3:112064200-112076800	Strong transcription	Placenta	Placenta
16	chr3:112064400-112075000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:112064400-112076800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:112064800-112077200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:112065600-112079600	Weak transcription	Fetal Intestine Large	intestine
20	chr3:112066000-112089800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:112066800-112076800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:112066800-112076800	Weak transcription	Ovary	ovary
23	chr3:112066800-112077000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:112067000-112079400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:112067200-112075400	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr3:112067200-112076800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:112067200-112079800	Weak transcription	Fetal Stomach	stomach
28	chr3:112067200-112080400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:112067400-112076800	Weak transcription	Aorta	Aorta
30	chr3:112068800-112074600	Enhancers	HUVEC	blood vessel
31	chr3:112069200-112076800	Weak transcription	Thymus	Thymus
32	chr3:112069200-112084000	Weak transcription	Fetal Kidney	kidney
33	chr3:112069200-112095400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:112069400-112075400	Strong transcription	GM12878-XiMat	blood
35	chr3:112070200-112086200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:112070600-112080400	Weak transcription	Brain Angular Gyrus	brain
37	chr3:112070600-112080400	Weak transcription	Brain Anterior Caudate	brain
38	chr3:112070600-112086200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:112070600-112088800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:112070800-112079600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:112070800-112084600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:112070800-112090600	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:112071000-112076200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:112071000-112076800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:112071000-112077600	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:112071000-112083000	Weak transcription	Brain Substantia Nigra	brain
47	chr3:112071200-112076400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:112071200-112083800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr3:112071800-112079400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:112072000-112080600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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