Variant report

Variant	rs7862467
Chromosome Location	chr9:3181278-3181279
allele	G/T
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	RAD21	chr9:3181147-3182127	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr9:3180967-3182072	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr9:3180949-3181432	ECC-1	luminal epithelium:	n/a	n/a
4	E2F6	chr9:3180957-3181919	H1-hESC	embryonic stem cell:	n/a	n/a
5	MYC	chr9:3181214-3181299	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr9:3180932-3182063	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr9:3181220-3181370	HBMEC	blood vessel:	n/a	chr9:3181294-3181303
8	MAX	chr9:3180982-3182013	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr9:3181260-3181410	HEK293	kidney:	n/a	chr9:3181294-3181303
10	CTCF	chr9:3181260-3181410	HRPEpiC	eye:	n/a	chr9:3181294-3181303
11	CTCF	chr9:3181220-3181370	HRE	kidney:	n/a	chr9:3181294-3181303
12	ZNF263	chr9:3180978-3181925	HEK293-T-REx	kidney:	n/a	chr9:3181288-3181297
13	CTCF	chr9:3181200-3181350	HEK293	kidney:	n/a	chr9:3181294-3181303
14	MAX	chr9:3180904-3182020	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr9:3181258-3181315	H1-hESC	embryonic stem cell:	n/a	chr9:3181294-3181303
16	CTBP2	chr9:3180996-3182245	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000236511	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10813628	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10813629	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10970482	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1885471	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7024687	0.82[EUR][1000 genomes]
rs7038505	0.81[EUR][1000 genomes]
rs7041489	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7869695	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892085	chr9:2937654-3215842	Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1017474	chr9:3019068-3247215	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv892088	chr9:3019383-3215842	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1028668	chr9:3139007-3262791	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv539939	chr9:3139007-3262791	Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7862467	AK3	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3180600-3181400	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr9:3180600-3181400	Active TSS	Brain Anterior Caudate	brain
3	chr9:3180600-3181800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
4	chr9:3180600-3182000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:3180600-3182200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr9:3180600-3182200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr9:3180600-3182200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr9:3180800-3181400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
9	chr9:3180800-3181400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:3180800-3181400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:3180800-3181600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:3180800-3181600	Active TSS	Colon Smooth Muscle	Colon
13	chr9:3180800-3181800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr9:3180800-3181800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
15	chr9:3180800-3181800	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr9:3180800-3181800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
19	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
22	chr9:3180800-3181800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
24	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
25	chr9:3180800-3182000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:3180800-3182000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr9:3180800-3182000	Bivalent Enhancer	Fetal Heart	heart
28	chr9:3180800-3182200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr9:3181000-3181400	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:3181000-3181400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:3181000-3181400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:3181000-3181400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
33	chr9:3181000-3181400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
34	chr9:3181000-3181400	Bivalent/Poised TSS	Fetal Kidney	kidney
35	chr9:3181000-3181400	Enhancers	Gastric	stomach
36	chr9:3181000-3181400	Bivalent/Poised TSS	NHLF	lung
37	chr9:3181000-3181600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:3181000-3181600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr9:3181000-3181600	Bivalent Enhancer	Spleen	Spleen
40	chr9:3181000-3181800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:3181000-3181800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr9:3181000-3181800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:3181000-3181800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
44	chr9:3181000-3181800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:3181000-3181800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr9:3181000-3181800	Enhancers	Liver	Liver
47	chr9:3181000-3181800	Active TSS	Brain Angular Gyrus	brain
48	chr9:3181000-3181800	Flanking Active TSS	Esophagus	oesophagus
49	chr9:3181000-3181800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
50	chr9:3181000-3181800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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