Variant report

Variant	rs10121164
Chromosome Location	chr9:115918552-115918553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115873156..115875899-chr9:115915858..115921312,4	MCF-7	breast:
2	chr9:115917061..115918640-chr9:115927400..115929607,2	MCF-7	breast:
3	chr9:115916286..115919484-chr9:115921664..115924647,3	K562	blood:
4	chr9:115913232..115915242-chr9:115917477..115919096,2	K562	blood:

Variant related genes	Relation type
ENSG00000136867	Chromatin interaction
ENSG00000231528	Chromatin interaction
ENSG00000225684	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10981652	0.80[ASN][1000 genomes]
rs3810908	0.85[LWK][hapmap];0.87[YRI][hapmap]
rs4263842	0.94[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs6477989	0.83[YRI][hapmap]
rs7028607	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831691	chr9:115754699-115929459	Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv1051654	chr9:115881588-115935663	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv466507	chr9:115905850-115936903	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv615213	chr9:115905850-115936903	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers 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 target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10121164	C9orf84	cis	cerebellum	SCAN
rs10121164	CDC26	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115914000-115923600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:115914000-115925000	Weak transcription	Fetal Kidney	kidney
3	chr9:115914200-115919400	Weak transcription	Fetal Stomach	stomach
4	chr9:115914200-115919600	Weak transcription	Fetal Lung	lung
5	chr9:115914200-115919600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:115914200-115920200	Weak transcription	Brain Germinal Matrix	brain
7	chr9:115914200-115922800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:115914200-115922800	Weak transcription	Fetal Heart	heart
9	chr9:115914200-115923600	Weak transcription	A549	lung
10	chr9:115914200-115923800	Weak transcription	HUVEC	blood vessel
11	chr9:115914400-115919200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr9:115914400-115920200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:115914400-115925000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr9:115914600-115920400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:115914800-115919400	Weak transcription	Fetal Intestine Large	intestine
16	chr9:115914800-115920600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr9:115914800-115926400	Weak transcription	Fetal Brain Male	brain
18	chr9:115915000-115919000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr9:115915000-115919000	Enhancers	Duodenum Mucosa	Duodenum
20	chr9:115915000-115919000	Weak transcription	Fetal Brain Female	brain
21	chr9:115915000-115919200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr9:115915000-115919600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:115915000-115919600	Weak transcription	Fetal Intestine Small	intestine
24	chr9:115915000-115919800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr9:115915000-115920000	Weak transcription	Esophagus	oesophagus
26	chr9:115915000-115920400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:115915000-115923000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:115915000-115923400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:115915000-115923600	Weak transcription	Colonic Mucosa	Colon
30	chr9:115915200-115920200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:115915200-115920600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:115915200-115923400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:115915200-115930200	Weak transcription	Stomach Mucosa	stomach
34	chr9:115915400-115918800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr9:115915400-115920400	Weak transcription	Gastric	stomach
36	chr9:115915400-115920600	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:115915400-115923400	Weak transcription	Hela-S3	cervix
38	chr9:115915400-115925200	Weak transcription	Small Intestine	intestine
39	chr9:115915800-115918800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr9:115916000-115918600	Genic enhancers	NHEK	skin
41	chr9:115916000-115919200	Genic enhancers	HMEC	breast
42	chr9:115916000-115919600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr9:115916200-115918800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:115916400-115918800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:115916600-115919000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:115916600-115919800	Enhancers	Fetal Thymus	thymus
47	chr9:115916800-115922200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr9:115917000-115919600	Weak transcription	Lung	lung
49	chr9:115917000-115921000	Weak transcription	NH-A	brain
50	chr9:115917200-115919000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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