Variant report

Variant	rs12080565
Chromosome Location	chr1:223905833-223905834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
2	chr1:223904423..223906015-chr1:223946207..223948782,2	K562	blood:
3	chr1:223904247..223905976-chr1:223916920..223919197,2	MCF-7	breast:
4	chr1:223895202..223897591-chr1:223904463..223906328,2	K562	blood:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10916601	0.95[ASN][1000 genomes]
rs10916602	0.95[ASN][1000 genomes]
rs10916604	0.91[ASN][1000 genomes]
rs11579787	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11580689	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11581716	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11588475	0.90[EUR][1000 genomes]
rs12057708	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12074091	0.95[ASN][1000 genomes]
rs16842040	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16842062	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1892077	0.86[CHB][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs2000320	0.91[ASN][1000 genomes]
rs2154113	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2186006	0.86[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs2275877	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28370012	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28370013	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28370014	0.95[ASN][1000 genomes]
rs28370020	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28370029	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4653499	0.95[ASN][1000 genomes]
rs61823966	0.95[ASN][1000 genomes]
rs6669046	0.83[ASN][1000 genomes]
rs6674733	0.83[ASN][1000 genomes]
rs7366009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7414311	0.95[ASN][1000 genomes]
rs7543197	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs7555491	0.86[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223900800-223906000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:223901400-223907600	Transcr. at gene 5' and 3'	A549	lung
3	chr1:223901600-223906200	Enhancers	Primary B cells from peripheral blood	blood
4	chr1:223901600-223906400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:223901800-223906200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:223902200-223913400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:223902400-223906200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:223902400-223906600	Enhancers	Fetal Thymus	thymus
9	chr1:223902600-223906000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:223902800-223914200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:223903000-223906000	Enhancers	Primary B cells from cord blood	blood
12	chr1:223903000-223907800	Weak transcription	Liver	Liver
13	chr1:223903200-223906400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:223903200-223907200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:223903200-223913600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:223903400-223906200	Strong transcription	Fetal Kidney	kidney
17	chr1:223903400-223907400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
18	chr1:223903400-223908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:223903400-223908800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:223903600-223909400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:223903600-223911800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:223903600-223922400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:223904000-223909000	Genic enhancers	Hela-S3	cervix
24	chr1:223904000-223910000	Genic enhancers	Osteobl	bone
25	chr1:223904200-223906800	Strong transcription	Fetal Lung	lung
26	chr1:223904200-223909800	Genic enhancers	NH-A	brain
27	chr1:223904400-223906000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:223904400-223906000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:223904400-223906000	Genic enhancers	Adipose Nuclei	Adipose
30	chr1:223904400-223906000	Genic enhancers	Lung	lung
31	chr1:223904400-223907400	Genic enhancers	HMEC	breast
32	chr1:223904400-223910000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:223904400-223913000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:223904400-223922400	Genic enhancers	NHLF	lung
35	chr1:223904600-223906000	Strong transcription	Fetal Intestine Small	intestine
36	chr1:223904600-223907200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:223904600-223907600	Weak transcription	Small Intestine	intestine
38	chr1:223904600-223908000	Weak transcription	Thymus	Thymus
39	chr1:223904600-223908600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:223904600-223908600	Weak transcription	Right Atrium	heart
41	chr1:223904600-223909800	Genic enhancers	HUVEC	blood vessel
42	chr1:223904600-223913600	Strong transcription	Brain Anterior Caudate	brain
43	chr1:223904600-223914000	Genic enhancers	NHDF-Ad	bronchial
44	chr1:223904800-223906000	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr1:223904800-223906200	Strong transcription	Fetal Intestine Large	intestine
46	chr1:223904800-223906400	Enhancers	Primary T cells from cord blood	blood
47	chr1:223904800-223907400	Strong transcription	K562	blood
48	chr1:223904800-223908000	Genic enhancers	Placenta	Placenta
49	chr1:223904800-223908400	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:223904800-223909000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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