Variant report

Variant	rs2797825
Chromosome Location	chr9:136629298-136629299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:136629161-136629400	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000256225	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2510244	0.89[ASN][1000 genomes]
rs2520002	0.89[ASN][1000 genomes]
rs2797826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478403	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs506278	0.89[ASN][1000 genomes]
rs556664	0.83[EUR][1000 genomes]
rs557430	1.00[JPT][hapmap]
rs581622	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs582682	0.89[ASN][1000 genomes]
rs591797	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs591866	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs592252	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs592820	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs593590	1.00[JPT][hapmap]
rs594130	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs653967	0.89[ASN][1000 genomes]
rs694174	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs694913	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894081	chr9:136227260-136678954	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv894086	chr9:136281753-136657960	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv530972	chr9:136324358-136643044	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv870051	chr9:136459745-136656889	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv894114	chr9:136538798-136779153	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv428546	chr9:136541745-136720872	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv831745	chr9:136593702-136780273	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv894117	chr9:136600201-136716399	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv831746	chr9:136607829-136750740	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv466622	chr9:136617292-136658816	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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
11	nsv615691	chr9:136617292-136658816	Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS 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
12	nsv894118	chr9:136624542-136678954	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	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
rs2797825	C9orf9	cis	parietal	SCAN
rs2797825	DOLK	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136619600-136631200	Weak transcription	Fetal Brain Male	brain
2	chr9:136620400-136632400	Weak transcription	NHDF-Ad	bronchial
3	chr9:136621200-136632600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:136622800-136631000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:136623000-136629600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:136623400-136629400	Strong transcription	Fetal Stomach	stomach
7	chr9:136623600-136631400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:136624000-136632800	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:136624400-136629400	Strong transcription	Fetal Intestine Small	intestine
10	chr9:136624400-136631600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr9:136624600-136630600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:136624600-136630600	Weak transcription	Right Atrium	heart
13	chr9:136624800-136632800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:136624800-136639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:136624800-136657800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr9:136625000-136632400	Weak transcription	A549	lung
17	chr9:136625200-136631200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:136625800-136630800	Strong transcription	Fetal Intestine Large	intestine
19	chr9:136625800-136632800	Strong transcription	Liver	Liver
20	chr9:136626000-136632200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:136626000-136637400	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr9:136626200-136630800	Strong transcription	Fetal Muscle Leg	muscle
23	chr9:136626200-136632400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:136626400-136636000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr9:136626600-136629400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:136626600-136629400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:136626600-136629400	Strong transcription	Lung	lung
28	chr9:136626600-136629400	Strong transcription	Pancreas	Pancrea
29	chr9:136626600-136629600	Strong transcription	Brain Germinal Matrix	brain
30	chr9:136626600-136629600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr9:136626600-136630000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
32	chr9:136626600-136630000	Strong transcription	NHEK	skin
33	chr9:136626600-136630400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:136626600-136631200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:136626600-136631400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr9:136626600-136632000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr9:136626600-136632400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:136626800-136632200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr9:136627000-136632000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr9:136627000-136632400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr9:136627000-136632600	Weak transcription	Aorta	Aorta
42	chr9:136627000-136632600	Weak transcription	Small Intestine	intestine
43	chr9:136627200-136632000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr9:136627400-136632800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:136627600-136629400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:136627600-136629400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr9:136627600-136629400	Strong transcription	NHLF	lung
48	chr9:136627600-136629600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr9:136627600-136629800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:136627600-136632600	Strong transcription	Primary monocytes fromperipheralblood	blood

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