Variant report

Variant	rs2560681
Chromosome Location	chr5:115368034-115368035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115175803..115178911-chr5:115366529..115369436,3	MCF-7	breast:
2	chr5:115223617..115224331-chr5:115367917..115368436,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145782	Chromatin interaction
ENSG00000177879	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1030464	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1030465	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1366205	0.90[EUR][1000 genomes]
rs1428090	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17138679	0.81[CHB][hapmap]
rs2115038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2244115	0.90[EUR][1000 genomes]
rs2560679	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2560680	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2560686	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2662447	0.92[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs2662448	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2662449	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs2662450	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2662451	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2662452	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2662453	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2662454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2662455	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2662457	0.90[EUR][1000 genomes]
rs2662458	0.89[EUR][1000 genomes]
rs2662459	0.88[EUR][1000 genomes]
rs872383	0.88[EUR][1000 genomes]
rs872384	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs956926	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs969558	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1027418	chr5:115206256-115446861	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv515611	chr5:115208843-115428381	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1021968	chr5:115213162-115426468	Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1024008	chr5:115222974-115431050	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1027117	chr5:115222974-115442883	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763487	chr5:115222986-115442895	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv462400	chr5:115223504-115428381	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv599478	chr5:115223504-115428381	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv1030480	chr5:115228889-115446861	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv599479	chr5:115233116-115450969	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv1029427	chr5:115236239-115387283	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
13	nsv1015976	chr5:115236239-115434163	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
14	nsv537868	chr5:115236239-115434163	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
15	nsv882735	chr5:115254723-115377150	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv882736	chr5:115254723-115552945	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
17	nsv882737	chr5:115263853-115552945	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2560681	YTHDC2	cis	cerebellum	SCAN
rs2560681	GPR109B	trans	lymphoblastoid	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115362200-115373600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr5:115366800-115368200	Enhancers	Hela-S3	cervix
3	chr5:115367000-115368200	Enhancers	Primary hematopoietic stem cells	blood
4	chr5:115367000-115368600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:115367400-115368200	Enhancers	Small Intestine	intestine
6	chr5:115367400-115368200	Enhancers	Osteobl	bone
7	chr5:115367400-115368400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr5:115367400-115368400	Enhancers	HSMM	muscle
9	chr5:115367600-115368200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:115367600-115368200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:115367600-115368200	Enhancers	HSMMtube	muscle
12	chr5:115367600-115368200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr5:115367600-115368200	Enhancers	NH-A	brain
14	chr5:115367600-115369600	Enhancers	Primary B cells from cord blood	blood
15	chr5:115367800-115368200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:115367800-115368200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:115367800-115368200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:115367800-115368200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr5:115367800-115368200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr5:115367800-115368200	Enhancers	Liver	Liver
21	chr5:115367800-115368200	Enhancers	Brain Substantia Nigra	brain
22	chr5:115367800-115368200	Active TSS	Duodenum Mucosa	Duodenum
23	chr5:115367800-115368200	Enhancers	Fetal Heart	heart
24	chr5:115367800-115368200	Enhancers	Fetal Lung	lung
25	chr5:115367800-115368200	Flanking Active TSS	A549	lung
26	chr5:115367800-115368200	Flanking Active TSS	GM12878-XiMat	blood
27	chr5:115367800-115368200	Enhancers	K562	blood
28	chr5:115367800-115368200	Enhancers	NHDF-Ad	bronchial
29	chr5:115368000-115368200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr5:115368000-115368200	Enhancers	Ovary	ovary
31	chr5:115368000-115368400	Enhancers	HUVEC	blood vessel
32	chr5:115368000-115371200	Enhancers	Primary B cells from peripheral blood	blood
33	chr5:115368000-115373000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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