Variant report

Variant	rs10869729
Chromosome Location	chr9:78808493-78808494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17062197	0.88[CHB][hapmap];0.82[MEX][hapmap]
rs17720593	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831627	chr9:78651134-78817669	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv893475	chr9:78753324-78817288	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv893476	chr9:78768830-78887992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10869729	ZFAND5	cis	cerebellum	SCAN
rs10869729	CEP78	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78790400-78810200	Weak transcription	Brain Angular Gyrus	brain
2	chr9:78790400-78810400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr9:78790400-78810400	Weak transcription	Brain Anterior Caudate	brain
4	chr9:78790400-78810400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:78790400-78811200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:78790400-78811400	Weak transcription	Fetal Lung	lung
7	chr9:78790400-78811400	Weak transcription	Right Ventricle	heart
8	chr9:78790400-78811600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:78790400-78813200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:78790400-78813600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr9:78790400-78818000	Weak transcription	Small Intestine	intestine
12	chr9:78794000-78809200	Strong transcription	Fetal Thymus	thymus
13	chr9:78794400-78814000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr9:78796400-78809200	Weak transcription	Gastric	stomach
15	chr9:78796400-78809800	Weak transcription	HSMMtube	muscle
16	chr9:78796400-78816200	Strong transcription	Fetal Intestine Large	intestine
17	chr9:78796400-78818200	Weak transcription	Fetal Heart	heart
18	chr9:78797000-78809600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:78797000-78809800	Weak transcription	NHLF	lung
20	chr9:78797000-78811200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr9:78797000-78812800	Weak transcription	Esophagus	oesophagus
22	chr9:78797000-78820800	Weak transcription	Pancreas	Pancrea
23	chr9:78797200-78808600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:78797200-78809400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:78797200-78809600	Weak transcription	NH-A	brain
26	chr9:78797200-78810200	Weak transcription	Stomach Mucosa	stomach
27	chr9:78797200-78810800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr9:78797200-78816400	Weak transcription	Fetal Stomach	stomach
29	chr9:78797200-78817000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr9:78797400-78821400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:78799800-78810400	Weak transcription	Colonic Mucosa	Colon
32	chr9:78801800-78811400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:78803000-78809000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr9:78803000-78813200	Strong transcription	Primary T cells from cord blood	blood
35	chr9:78803200-78809800	Strong transcription	Ovary	ovary
36	chr9:78803200-78816200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr9:78803400-78809200	Strong transcription	Thymus	Thymus
38	chr9:78803400-78810200	Strong transcription	Adipose Nuclei	Adipose
39	chr9:78803400-78814600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr9:78803600-78809000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr9:78803600-78810400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr9:78803800-78809600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:78804000-78810400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:78804800-78808600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:78804800-78811000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr9:78804800-78816000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:78806200-78811200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr9:78806600-78808800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:78806600-78811800	Weak transcription	Dnd41	blood
50	chr9:78807000-78809600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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