Variant report

Variant	rs10116020
Chromosome Location	chr9:8499960-8499961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10115201	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10115554	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10124277	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1323592	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs13286908	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13290896	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs13292865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13296910	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13298803	0.84[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13301979	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs16928002	1.00[CEU][hapmap]
rs16928048	1.00[CEU][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16928053	0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16928058	0.85[CHB][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17650289	0.82[EUR][1000 genomes]
rs2296102	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs34190427	0.87[EUR][1000 genomes]
rs34599557	0.93[EUR][1000 genomes]
rs35441574	0.87[EUR][1000 genomes]
rs35777094	0.89[EUR][1000 genomes]
rs35929428	0.86[EUR][1000 genomes]
rs4409447	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4495488	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4549838	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62534039	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62534040	0.95[EUR][1000 genomes]
rs7863060	0.87[CEU][hapmap];0.92[CHB][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv892226	chr9:8435525-8522326	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv892229	chr9:8485201-8520366	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv831504	chr9:8496277-8665773	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
2	chr9:8442200-8522200	Weak transcription	Liver	Liver
3	chr9:8478200-8504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:8479200-8504000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:8481200-8500800	Weak transcription	Fetal Intestine Small	intestine
6	chr9:8483800-8524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:8486000-8508400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:8486000-8519400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr9:8486000-8522200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:8486200-8501800	Weak transcription	Fetal Heart	heart
11	chr9:8486200-8504600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:8486200-8509000	Weak transcription	Brain Anterior Caudate	brain
13	chr9:8486200-8517200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:8486200-8522800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:8486200-8523200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:8486200-8531600	Weak transcription	Fetal Kidney	kidney
17	chr9:8486600-8507200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:8487000-8521200	Weak transcription	Brain Germinal Matrix	brain
19	chr9:8487000-8521200	Weak transcription	Dnd41	blood
20	chr9:8492400-8503400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:8492400-8504200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:8492400-8528800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:8492600-8503400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:8493000-8518000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:8493000-8521200	Weak transcription	Fetal Muscle Leg	muscle
26	chr9:8493200-8500800	Weak transcription	Pancreas	Pancrea
27	chr9:8493200-8523200	Weak transcription	Fetal Stomach	stomach
28	chr9:8493200-8531200	Weak transcription	Fetal Brain Female	brain
29	chr9:8494200-8531200	Weak transcription	Fetal Brain Male	brain
30	chr9:8494600-8503600	Weak transcription	Brain Angular Gyrus	brain
31	chr9:8494600-8506800	Weak transcription	Brain Hippocampus Middle	brain
32	chr9:8495000-8507000	Weak transcription	Brain Substantia Nigra	brain
33	chr9:8495000-8517800	Weak transcription	Ovary	ovary
34	chr9:8495600-8520400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:8497000-8500600	Weak transcription	Fetal Lung	lung
36	chr9:8498400-8501000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:8498400-8501600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:8499000-8501000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:8499400-8500600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:8499600-8501000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr9:8499800-8517600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links