Variant report

Variant	rs12346540
Chromosome Location	chr9:117791617-117791618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10817701	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10982497	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10982503	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10982504	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10982509	0.85[ASN][1000 genomes]
rs11788513	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11792749	0.85[EUR][1000 genomes]
rs12338715	0.84[ASN][1000 genomes]
rs12343737	0.89[ASN][1000 genomes]
rs12347433	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349585	0.85[ASN][1000 genomes]
rs12351083	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13285041	0.81[ASN][1000 genomes]
rs13286217	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411453	0.89[ASN][1000 genomes]
rs1411455	0.84[ASN][1000 genomes]
rs2297179	0.85[ASN][1000 genomes]
rs2297181	0.85[ASN][1000 genomes]
rs28491824	0.85[ASN][1000 genomes]
rs34690752	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34865477	0.81[ASN][1000 genomes]
rs3789875	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4452883	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7859478	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	esv1840787	chr9:117787173-117803882	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv1826575	chr9:117787173-117805719	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117773400-117803200	Weak transcription	Esophagus	oesophagus
2	chr9:117781800-117797400	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:117781800-117798200	Weak transcription	Fetal Intestine Large	intestine
4	chr9:117781800-117798400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:117781800-117808600	Weak transcription	Fetal Intestine Small	intestine
6	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
7	chr9:117783200-117792400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr9:117783200-117796800	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:117786200-117794800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:117786400-117794800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:117786600-117796600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:117786800-117792600	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:117787600-117792400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:117788000-117796600	Strong transcription	NH-A	brain
15	chr9:117788200-117794600	Strong transcription	Colon Smooth Muscle	Colon
16	chr9:117788200-117794800	Strong transcription	Osteobl	bone
17	chr9:117788400-117791800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:117788400-117795000	Strong transcription	Stomach Smooth Muscle	stomach
19	chr9:117788400-117797400	Weak transcription	Spleen	Spleen
20	chr9:117788600-117791800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr9:117788800-117796600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:117789000-117792400	Weak transcription	Lung	lung
23	chr9:117789000-117792600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:117789000-117808600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:117789600-117797400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr9:117789800-117797400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:117790000-117797400	Strong transcription	NHDF-Ad	bronchial
28	chr9:117790200-117796200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:117790800-117791800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:117790800-117791800	Enhancers	HMEC	breast
31	chr9:117791200-117791800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:117791200-117793800	Strong transcription	Rectal Smooth Muscle	rectum
33	chr9:117791200-117796800	Strong transcription	NHLF	lung
34	chr9:117791400-117791800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:117791400-117791800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:117791400-117791800	Enhancers	HSMM	muscle
37	chr9:117791400-117791800	Genic enhancers	NHEK	skin
38	chr9:117791400-117792000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:117791400-117792000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:117791400-117792800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr9:117791600-117792000	Strong transcription	Fetal Lung	lung
42	chr9:117791600-117792600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:117791600-117792800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:117791600-117793400	Strong transcription	Aorta	Aorta
45	chr9:117791600-117793600	Strong transcription	Fetal Kidney	kidney
46	chr9:117791600-117793800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:117791600-117794400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr9:117791600-117796600	Strong transcription	Fetal Stomach	stomach
49	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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