Variant report

Variant	rs2297568
Chromosome Location	chr9:94874651-94874652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94833215..94835590-chr9:94874330..94876455,2	K562	blood:
2	chr9:94853538..94856394-chr9:94873411..94875546,2	K562	blood:
3	chr9:94871544..94874605-chr9:94874619..94877875,5	MCF-7	breast:
4	chr9:94871412..94875028-chr9:94875797..94879228,6	K562	blood:

Variant related genes	Relation type
ENSG00000240791	Chromatin interaction
ENSG00000227321	Chromatin interaction
ENSG00000238288	Chromatin interaction
ENSG00000090054	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10116249	0.82[EUR][1000 genomes]
rs10118072	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10124760	0.82[EUR][1000 genomes]
rs10125466	0.90[TSI][hapmap]
rs10512220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10733743	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10739924	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10739925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761138	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10761143	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10820931	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820936	0.82[JPT][hapmap]
rs10820937	0.82[JPT][hapmap]
rs10992234	0.81[JPT][hapmap]
rs12340044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1316268	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1881391	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1892268	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1919100	0.81[EUR][1000 genomes]
rs1964170	0.87[CHB][hapmap]
rs1970121	0.82[JPT][hapmap]
rs2895201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3847308	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3858095	0.87[CHB][hapmap]
rs6479386	0.82[TSI][hapmap]
rs6479387	0.91[ASW][hapmap];0.88[CEU][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs6479388	0.83[EUR][1000 genomes]
rs6479389	0.91[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs6479400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6479402	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7020136	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7023075	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs7029539	0.82[JPT][hapmap]
rs7034357	0.88[EUR][1000 genomes]
rs7034363	0.85[EUR][1000 genomes]
rs7035867	0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7037255	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs7037848	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7038017	0.88[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs7041193	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7042102	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7046430	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7047326	0.85[EUR][1000 genomes]
rs7048339	0.84[ASN][1000 genomes]
rs7048699	0.83[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs7848874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7848987	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7852032	0.88[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs7856177	0.82[JPT][hapmap]
rs7859570	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7859689	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7860518	0.86[JPT][hapmap]
rs7863167	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs7867072	0.91[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7869504	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7871444	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9774945	0.84[GIH][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active 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 miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2297568	SPTLC1	cis	parietal	SCAN
rs2297568	FBP1	cis	parietal	SCAN
rs2297568	CDK20	cis	parietal	SCAN
rs2297568	ZNF484	cis	parietal	SCAN
rs2297568	ZNF484	cis	cerebellum	SCAN
rs2297568	FANCC	cis	cerebellum	SCAN
rs2297568	OMD	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94817800-94877000	Weak transcription	Fetal Heart	heart
2	chr9:94842800-94876600	Weak transcription	Colonic Mucosa	Colon
3	chr9:94851400-94876600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:94857000-94875400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr9:94860800-94876000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:94860800-94876000	Weak transcription	Brain Substantia Nigra	brain
7	chr9:94860800-94877000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:94860800-94877200	Weak transcription	Stomach Mucosa	stomach
9	chr9:94861000-94875000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr9:94861000-94876800	Weak transcription	Fetal Kidney	kidney
11	chr9:94861200-94876000	Weak transcription	Brain Hippocampus Middle	brain
12	chr9:94861400-94875600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr9:94861600-94875800	Weak transcription	Fetal Brain Male	brain
14	chr9:94861600-94877000	Weak transcription	Small Intestine	intestine
15	chr9:94863000-94876800	Weak transcription	HSMMtube	muscle
16	chr9:94863200-94876800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:94863600-94875800	Weak transcription	NHEK	skin
18	chr9:94864000-94875200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr9:94864200-94876000	Weak transcription	Hela-S3	cervix
20	chr9:94864400-94875000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:94864400-94875000	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:94864600-94875600	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:94864600-94876800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:94864800-94875000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:94864800-94876200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:94865400-94874800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr9:94865600-94874800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr9:94865600-94875000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:94865600-94875400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:94866200-94874800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:94866200-94875000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:94866200-94876600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr9:94866400-94875000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:94866600-94875800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:94866800-94876000	Weak transcription	A549	lung
36	chr9:94866800-94877000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:94867600-94874800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:94868000-94876800	Weak transcription	Pancreas	Pancrea
39	chr9:94868200-94875000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr9:94868200-94876200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:94868200-94876200	Weak transcription	Fetal Muscle Leg	muscle
42	chr9:94868200-94876200	Weak transcription	Right Ventricle	heart
43	chr9:94868200-94876400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr9:94868200-94876800	Weak transcription	Brain Angular Gyrus	brain
45	chr9:94868400-94875600	Weak transcription	Brain Germinal Matrix	brain
46	chr9:94868400-94876200	Weak transcription	Esophagus	oesophagus
47	chr9:94868400-94876400	Weak transcription	Lung	lung
48	chr9:94868400-94877000	Weak transcription	Aorta	Aorta
49	chr9:94868600-94875800	Weak transcription	Fetal Brain Female	brain
50	chr9:94868600-94876200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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