Variant report

Variant	rs4560868
Chromosome Location	chr9:115985499-115985500
allele	C/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	ZNF384	chr9:115985397-115985591	K562	blood:	n/a	n/a
2	JUN	chr9:115982833-115985815	K562	blood:	n/a	chr9:115983457-115983467 chr9:115984985-115984998 chr9:115983731-115983740

No.	Distal block	Cell Line	Cell type
1	chr9:115981728..115986983-chr9:116035777..116040437,9	K562	blood:
2	chr9:115980360..115986264-chr9:116170629..116175189,6	K562	blood:
3	chr9:115983607..115986374-chr9:116170251..116172763,3	MCF-7	breast:
4	chr9:115982005..115986983-chr9:116035777..116039702,5	K562	blood:

Variant related genes	Relation type
FKBP15	TF binding region
ENSG00000136875	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000157653	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10123415	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125992	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513189	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739388	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739390	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739392	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10759633	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759636	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759637	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759638	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs10817461	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817468	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981715	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs11789755	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs11792628	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12343629	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs2296073	0.82[CHB][hapmap]
rs3750532	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs3750533	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs3750534	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs4129395	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4129396	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4129397	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4284098	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979223	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979226	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979231	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs6477998	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477999	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7022397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7038769	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7041615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850357	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7859354	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9299214	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1041112	chr9:115960704-116005783	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv893746	chr9:115983540-116022826	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4560868	CDC26	cis	Esophagus Muscularis	GTEx
rs4560868	ZNF618	cis	cerebellum	SCAN
rs4560868	CDC26	cis	Muscle Skeletal	GTEx
rs4560868	CDC26	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115981200-115985600	Active TSS	GM12878-XiMat	blood
2	chr9:115982200-115985600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:115982600-115985600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:115984200-115985800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr9:115984400-115985800	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr9:115984400-115986400	Flanking Active TSS	Liver	Liver
7	chr9:115984400-115986600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:115984600-115985600	Flanking Active TSS	HMEC	breast
9	chr9:115984600-115985800	Flanking Active TSS	NHEK	skin
10	chr9:115984800-115985600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr9:115984800-115985600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr9:115984800-115985800	Enhancers	Placenta	Placenta
13	chr9:115984800-115985800	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr9:115984800-115985800	Enhancers	Stomach Mucosa	stomach
15	chr9:115984800-115985800	Flanking Active TSS	Hela-S3	cervix
16	chr9:115984800-115985800	Transcr. at gene 5' and 3'	K562	blood
17	chr9:115984800-115994800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr9:115984800-115995400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:115985000-115985600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:115985000-115985600	Enhancers	Gastric	stomach
21	chr9:115985000-115985800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr9:115985000-115985800	Enhancers	Fetal Stomach	stomach
23	chr9:115985000-115985800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr9:115985000-115987000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:115985000-115990200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr9:115985000-115994600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr9:115985000-115994600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr9:115985000-115994800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr9:115985000-115994800	Weak transcription	Left Ventricle	heart
30	chr9:115985000-115996200	Weak transcription	Brain Substantia Nigra	brain
31	chr9:115985000-116020800	Weak transcription	Aorta	Aorta
32	chr9:115985200-115985600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:115985200-115985600	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr9:115985200-115985600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr9:115985200-115985600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:115985200-115985600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr9:115985200-115985600	Enhancers	Brain Germinal Matrix	brain
38	chr9:115985200-115985600	Enhancers	Brain Hippocampus Middle	brain
39	chr9:115985200-115985600	Enhancers	HSMM	muscle
40	chr9:115985200-115985600	Enhancers	NH-A	brain
41	chr9:115985200-115985600	Active TSS	NHDF-Ad	bronchial
42	chr9:115985200-115985600	Active TSS	NHLF	lung
43	chr9:115985200-115985800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:115985200-115985800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:115985200-115985800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:115985200-115985800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:115985200-115985800	Enhancers	Colon Smooth Muscle	Colon
48	chr9:115985200-115985800	Enhancers	Fetal Intestine Small	intestine
49	chr9:115985200-115985800	Enhancers	Psoas Muscle	Psoas
50	chr9:115985200-115985800	Enhancers	Stomach Smooth Muscle	stomach

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