Variant report

Variant	rs12683163
Chromosome Location	chr9:117815011-117815012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DEC1-5	chr9:117814727-117815065	NONHSAT134407

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16932058	1.00[EUR][1000 genomes]
rs16932066	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16932085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274754	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34166409	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748172	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789876	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57060600	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60347203	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60687796	1.00[EUR][1000 genomes]
rs73656713	1.00[EUR][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

No data

Chromatin state (count:43 , 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	chr9:117799200-117819800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:117799400-117817000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:117800800-117825000	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:117800800-117825200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:117801000-117819200	Weak transcription	HMEC	breast
8	chr9:117801800-117820200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
10	chr9:117803400-117820000	Weak transcription	Aorta	Aorta
11	chr9:117803400-117820600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:117803600-117820200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:117803600-117825400	Weak transcription	Fetal Kidney	kidney
14	chr9:117805800-117818800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:117806800-117816800	Strong transcription	Osteobl	bone
16	chr9:117807200-117816800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:117807400-117819600	Strong transcription	NHDF-Ad	bronchial
18	chr9:117807400-117819800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:117807600-117817400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:117809000-117825400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:117809200-117821000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:117809800-117815200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:117810000-117817600	Weak transcription	Fetal Stomach	stomach
24	chr9:117810200-117817600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:117810600-117825000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:117811000-117816600	Weak transcription	Colon Smooth Muscle	Colon
27	chr9:117811800-117816800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:117812800-117819200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:117812800-117825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:117812800-117830600	Weak transcription	Fetal Lung	lung
31	chr9:117813000-117817000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:117813000-117817600	Weak transcription	NHEK	skin
33	chr9:117813200-117825000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr9:117813600-117819200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:117813800-117815200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
36	chr9:117813800-117816800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:117814200-117815200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:117814400-117818000	Strong transcription	NHLF	lung
39	chr9:117815000-117815200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:117815000-117815200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:117815000-117815400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr9:117815000-117815400	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr9:117815000-117815400	Strong transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links