Variant report

Variant	rs618145
Chromosome Location	chr9:79319560-79319561
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:83)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:83 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr9:79319514-79319801	K562	blood:	n/a	n/a
2	MAFF	chr9:79319488-79319793	HepG2	liver:	n/a	n/a
3	CTCF	chr9:79319423-79319922	MCF-7	breast:	n/a	n/a
4	CTCF	chr9:79319480-79319630	HFF-Myc	foreskin:	n/a	n/a
5	RAD21	chr9:79319416-79320021	HCT-116	colon:	n/a	n/a
6	FOS	chr9:79319533-79319732	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr9:79319480-79319630	A549	lung:	n/a	n/a
8	CTCF	chr9:79319551-79319861	Spleen_OC	spleen:	n/a	n/a
9	STAT3	chr9:79319507-79319711	MCF10A-Er-Src	breast:	n/a	chr9:79319642-79319653 chr9:79319641-79319655
10	CTCF	chr9:79319560-79319710	Hela-S3	cervix:	n/a	n/a
11	SMC3	chr9:79319517-79319841	K562	blood:	n/a	n/a
12	RAD21	chr9:79319397-79320042	A549	lung:	n/a	n/a
13	CTCF	chr9:79319539-79319857	SK-N-SH_RA	brain:	n/a	n/a
14	RAD21	chr9:79319478-79319905	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr9:79319407-79320050	HCT-116	colon:	n/a	n/a
16	CTCF	chr9:79319550-79319808	A549	lung:	n/a	n/a
17	RAD21	chr9:79319410-79319893	SK-N-SH_RA	brain:	n/a	n/a
18	RAD21	chr9:79319464-79319928	A549	lung:	n/a	n/a
19	JUND	chr9:79319533-79319821	K562	blood:	n/a	n/a
20	CTCF	chr9:79319448-79319897	H1-hESC	embryonic stem cell:	n/a	n/a
21	RAD21	chr9:79319414-79319877	SK-N-SH_RA	brain:	n/a	n/a
22	CTCF	chr9:79319546-79319848	HepG2	liver:	n/a	n/a
23	CTCF	chr9:79319496-79319890	ECC-1	luminal epithelium:	n/a	n/a
24	STAT3	chr9:79319514-79319816	MCF10A-Er-Src	breast:	n/a	chr9:79319642-79319653 chr9:79319641-79319655
25	CTCF	chr9:79319353-79320142	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr9:79319560-79319835	HUVEC	blood vessel:	n/a	n/a
27	RAD21	chr9:79319503-79319867	A549	lung:	n/a	n/a
28	CTCF	chr9:79319500-79319650	Caco-2	colon:	n/a	n/a
29	RAD21	chr9:79319501-79319874	K562	blood:	n/a	n/a
30	CTCF	chr9:79319556-79319824	Hela-S3	cervix:	n/a	n/a
31	RAD21	chr9:79319259-79320092	SK-N-SH	brain:	n/a	n/a
32	SMC3	chr9:79319472-79319935	Hela-S3	cervix:	n/a	n/a
33	RAD21	chr9:79319335-79319960	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr9:79319399-79319900	MCF-7	breast:	n/a	n/a
35	RAD21	chr9:79319473-79319913	GM12878	blood:	n/a	n/a
36	CTCF	chr9:79319480-79319903	K562	blood:	n/a	n/a
37	RAD21	chr9:79319416-79319966	ECC-1	luminal epithelium:	n/a	n/a
38	KAP1	chr9:79319470-79319954	HEK293	kidney:	n/a	n/a
39	RAD21	chr9:79319379-79319967	HepG2	liver:	n/a	n/a
40	CTCF	chr9:79319522-79319802	ECC-1	luminal epithelium:	n/a	n/a
41	RAD21	chr9:79319320-79320007	ECC-1	luminal epithelium:	n/a	n/a
42	CTCF	chr9:79319500-79319650	HFF	foreskin:	n/a	n/a
43	FOS	chr9:79319543-79319745	MCF10A-Er-Src	breast:	n/a	n/a
44	RAD21	chr9:79319439-79319924	H1-hESC	embryonic stem cell:	n/a	n/a
45	SMC3	chr9:79319495-79319933	GM12878	blood:	n/a	n/a
46	BRCA1	chr9:79319550-79319818	H1-hESC	embryonic stem cell:	n/a	n/a
47	ZNF143	chr9:79319519-79319868	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr9:79319317-79320447	A549	lung:	n/a	n/a
49	RAD21	chr9:79319402-79320054	HCT-116	colon:	n/a	n/a
50	CTCF	chr9:79319462-79319864	HCT-116	colon:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:79062552..79063515-chr9:79319220..79320201,4	K562	blood:
2	chr9:77880081..77881018-chr9:79319218..79320052,2	K562	blood:
3	chr9:79017921..79018920-chr9:79318594..79320251,5	K562	blood:
4	chr9:79277119..79278141-chr9:79318359..79319673,4	MCF-7	breast:
5	chr9:79280331..79281278-chr9:79319093..79320181,5	MCF-7	breast:
6	chr9:79280654..79281415-chr9:79319254..79320174,3	K562	blood:

No data

Variant related genes	Relation type
PRUNE2	TF binding region
ENSG00000265488	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10869799	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500952	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505034	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs506086	0.81[CEU][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs509489	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs512110	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554143	0.82[EUR][1000 genomes]
rs556725	0.93[CEU][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs560094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561970	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[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];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566584	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572737	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591411	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594586	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs611461	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs615187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs620321	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[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];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625981	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs626416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs646698	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650682	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs677913	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs678943	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs680729	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018971	0.82[EUR][1000 genomes]
rs7033337	0.86[EUR][1000 genomes]
rs7033978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870516	1.00[JPT][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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv2754389	chr9:79318677-79333056	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs618145	FAM108B1	cis	parietal	SCAN
rs618145	KIAA0367	cis	multi-tissue	Pritchard
rs618145	C9orf85	cis	parietal	SCAN
rs618145	PRUNE2	cis	Whole Blood	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79314200-79320000	Enhancers	Fetal Brain Male	brain
3	chr9:79315200-79319600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr9:79315200-79327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:79316200-79330800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:79316400-79319800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:79316400-79332000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:79316600-79324600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:79316800-79319800	Weak transcription	Brain Anterior Caudate	brain
10	chr9:79316800-79322800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:79316800-79325400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:79316800-79331000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:79316800-79331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:79317200-79319600	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:79317400-79319800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr9:79317400-79327800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:79317400-79328600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:79317600-79320000	Weak transcription	Aorta	Aorta
19	chr9:79317600-79330800	Strong transcription	HSMM	muscle
20	chr9:79317800-79328600	Strong transcription	HSMMtube	muscle
21	chr9:79318000-79330400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:79318400-79319800	Enhancers	HUVEC	blood vessel
23	chr9:79318400-79330000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:79318800-79319800	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:79318800-79319800	Weak transcription	Fetal Stomach	stomach
26	chr9:79318800-79319800	Weak transcription	Fetal Thymus	thymus
27	chr9:79318800-79320000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr9:79318800-79323200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:79319000-79319800	Weak transcription	Brain Substantia Nigra	brain
30	chr9:79319200-79319800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr9:79319400-79319600	Enhancers	Stomach Mucosa	stomach
32	chr9:79319400-79319600	Enhancers	NHDF-Ad	bronchial
33	chr9:79319400-79320000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:79319400-79320000	Enhancers	Primary hematopoietic stem cells	blood
35	chr9:79319400-79320000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:79319400-79320000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:79319400-79320000	Enhancers	Brain Angular Gyrus	brain
38	chr9:79319400-79320000	Enhancers	Fetal Kidney	kidney
39	chr9:79319400-79320200	Enhancers	Colon Smooth Muscle	Colon

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