Variant report

Variant	rs15580
Chromosome Location	chr6:26546048-26546049
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	chr6:26283512..26285254-chr6:26544162..26546329,2	K562	blood:
2	chr6:26541650..26546578-chr6:26547247..26553909,5	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1535278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes]
rs1796524	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes]
rs2145319	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2224379	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736780	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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3864291	1.00[JPT][hapmap]
rs4713007	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];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];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6905163	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6911330	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6922256	0.83[LWK][hapmap]
rs6927012	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes]
rs6929908	0.87[LWK][hapmap];1.00[MKK][hapmap]
rs7745632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9295697	0.95[EUR][1000 genomes]
rs9366661	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9379892	0.87[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers 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	1215 gene(s)	inside rSNPs	diseases
3	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs15580	HIST1H4F	cis	cerebellum	SCAN
rs15580	HMGN4	cis	parietal	SCAN
rs15580	ZSCAN23	cis	cerebellum	SCAN
rs15580	RP11-457M11.5	cis	Adipose Subcutaneous	GTEx
rs15580	RP11-457M11.5	cis	Artery Aorta	GTEx
rs15580	RP11-457M11.5	cis	Thyroid	GTEx
rs15580	HIST1H2BN	cis	parietal	SCAN
rs15580	RP11-457M11.5	cis	lung	GTEx
rs15580	ABT1	cis	cerebellum	SCAN
rs15580	HIST1H3E	cis	parietal	SCAN
rs15580	RP11-457M11.5	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26539200-26550600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:26539400-26550600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:26539600-26549800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:26539600-26550400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:26539600-26550400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:26539600-26550400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:26539600-26550600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:26539600-26553000	Weak transcription	Fetal Heart	heart
9	chr6:26539800-26550400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:26539800-26550400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:26539800-26550800	Weak transcription	Pancreas	Pancrea
12	chr6:26540000-26550800	Weak transcription	Lung	lung
13	chr6:26540200-26550000	Weak transcription	Fetal Kidney	kidney
14	chr6:26540200-26550400	Weak transcription	Colonic Mucosa	Colon
15	chr6:26540400-26546400	Strong transcription	Adipose Nuclei	Adipose
16	chr6:26540400-26547200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:26540400-26548000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:26540400-26550000	Weak transcription	Stomach Mucosa	stomach
19	chr6:26540400-26550400	Weak transcription	Brain Angular Gyrus	brain
20	chr6:26540400-26550400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:26540400-26550600	Weak transcription	Brain Substantia Nigra	brain
22	chr6:26540600-26548800	Weak transcription	Fetal Brain Male	brain
23	chr6:26540600-26550000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:26540600-26550000	Weak transcription	Small Intestine	intestine
25	chr6:26541000-26546200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr6:26541200-26546200	Strong transcription	NHDF-Ad	bronchial
27	chr6:26541400-26547400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:26541600-26547400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:26541800-26547000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr6:26541800-26547000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:26542000-26550600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:26542200-26550000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr6:26542400-26546400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:26542400-26546400	Strong transcription	HSMM	muscle
35	chr6:26542400-26547000	Strong transcription	Placenta	Placenta
36	chr6:26542600-26546400	Strong transcription	Primary B cells from cord blood	blood
37	chr6:26542600-26546400	Strong transcription	NHEK	skin
38	chr6:26542600-26546600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:26542600-26547000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:26542600-26547000	Strong transcription	Fetal Brain Female	brain
41	chr6:26542600-26547000	Strong transcription	Fetal Thymus	thymus
42	chr6:26542600-26547400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:26542600-26547400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:26542600-26547400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:26542800-26546800	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr6:26542800-26547400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:26543000-26546200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:26543000-26546400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:26543000-26546800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:26543200-26547400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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