Variant report

Variant	rs16932160
Chromosome Location	chr9:117829987-117829988
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1060545	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1330368	0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs5010187	0.84[ASN][1000 genomes]
rs7865462	0.82[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16932160	C9orf29	cis	parietal	SCAN
rs16932160	OR2K2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
4	chr9:117812800-117830600	Weak transcription	Fetal Lung	lung
5	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:117817800-117850600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:117819800-117848000	Weak transcription	Fetal Intestine Small	intestine
8	chr9:117821400-117840200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:117822400-117854400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:117825400-117848000	Weak transcription	Lung	lung
11	chr9:117826000-117830600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:117826000-117834200	Weak transcription	Fetal Kidney	kidney
13	chr9:117826400-117833600	Weak transcription	HSMMtube	muscle
14	chr9:117826400-117834400	Weak transcription	Esophagus	oesophagus
15	chr9:117826400-117835800	Weak transcription	Aorta	Aorta
16	chr9:117826600-117835600	Weak transcription	HMEC	breast
17	chr9:117826800-117849400	Strong transcription	Osteobl	bone
18	chr9:117827000-117834800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:117827000-117834800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:117827000-117848600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr9:117827000-117849200	Strong transcription	NHDF-Ad	bronchial
22	chr9:117827200-117830400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:117827200-117832400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:117827200-117832400	Weak transcription	NHEK	skin
25	chr9:117827200-117832600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr9:117827200-117834200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr9:117827200-117834400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:117827200-117835800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:117827200-117855200	Strong transcription	NH-A	brain
30	chr9:117827400-117832400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:117827400-117832600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:117827400-117832600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:117827400-117834400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:117827400-117849200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:117828000-117830200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:117828000-117830400	Enhancers	Colon Smooth Muscle	Colon
37	chr9:117828000-117832400	Weak transcription	Fetal Stomach	stomach
38	chr9:117828000-117832600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:117828200-117832400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:117828200-117833800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:117828400-117831800	Enhancers	Rectal Smooth Muscle	rectum
42	chr9:117828800-117833600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:117829000-117830600	Weak transcription	Fetal Muscle Leg	muscle
44	chr9:117829200-117830400	Enhancers	Stomach Smooth Muscle	stomach
45	chr9:117829400-117830400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:117829400-117839200	Strong transcription	NHLF	lung
47	chr9:117829800-117831600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:117829800-117838400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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