Variant report

Variant	rs10122193
Chromosome Location	chr9:15154647-15154648
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TTC39B-2	chr9:15153622-15156031	ucscGeneNc_uc003zlo_1

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10122198	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10738388	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10810354	0.92[EUR][1000 genomes]
rs10810356	0.90[EUR][1000 genomes]
rs10810357	0.90[EUR][1000 genomes]
rs1620257	0.83[AMR][1000 genomes]
rs1780149	0.90[AMR][1000 genomes]
rs1853479	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2057480	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2096366	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2506759	0.83[AMR][1000 genomes]
rs2761129	0.81[AMR][1000 genomes]
rs2761135	0.83[AMR][1000 genomes]
rs2761139	0.88[AMR][1000 genomes]
rs2800577	0.83[AMR][1000 genomes]
rs2800587	0.87[EUR][1000 genomes]
rs2800588	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35697804	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4741472	0.84[EUR][1000 genomes]
rs4741473	0.85[EUR][1000 genomes]
rs932712	0.83[AMR][1000 genomes]
rs932713	0.85[AMR][1000 genomes]
rs971834	0.94[MEX][hapmap];0.86[TSI][hapmap]
rs971835	0.94[MEX][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831519	chr9:15018160-15209127	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1019567	chr9:15031398-15159409	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10122193	ZDHHC21	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15137200-15156000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:15146800-15160400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:15147200-15156400	Weak transcription	Fetal Brain Male	brain
4	chr9:15148000-15155400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:15151000-15156400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:15151400-15155400	Weak transcription	Osteobl	bone
7	chr9:15151800-15154800	Weak transcription	HUVEC	blood vessel
8	chr9:15152600-15157600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:15153000-15157200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:15153600-15155200	Enhancers	Aorta	Aorta
11	chr9:15153600-15155200	Enhancers	Right Atrium	heart
12	chr9:15153600-15155600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr9:15153800-15154800	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:15154000-15156000	Weak transcription	Fetal Muscle Leg	muscle
15	chr9:15154400-15155200	Enhancers	Fetal Stomach	stomach
16	chr9:15154400-15155200	Enhancers	Ovary	ovary
17	chr9:15154600-15154800	Weak transcription	Fetal Brain Female	brain
18	chr9:15154600-15154800	Enhancers	Left Ventricle	heart
19	chr9:15154600-15155000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr9:15154600-15155000	Enhancers	Stomach Smooth Muscle	stomach
21	chr9:15154600-15155200	Enhancers	Psoas Muscle	Psoas
22	chr9:15154600-15155400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr9:15154600-15155600	Enhancers	Rectal Smooth Muscle	rectum
24	chr9:15154600-15155800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr9:15154600-15156800	Enhancers	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links