Variant report

Variant	rs6005425
Chromosome Location	chr22:27816110-27816111
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:27813673..27816169-chr22:27820833..27822951,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12158509	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12160663	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13054757	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs136940	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs136941	0.80[EUR][1000 genomes]
rs136942	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs136944	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs136945	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs136948	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs136949	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs136950	0.83[EUR][1000 genomes]
rs136955	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs136956	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs136961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884127	0.87[ASN][1000 genomes]
rs1884128	0.87[ASN][1000 genomes]
rs1884129	0.87[ASN][1000 genomes]
rs2342940	0.82[EUR][1000 genomes]
rs34716864	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4822876	0.87[ASN][1000 genomes]
rs5752544	0.87[ASN][1000 genomes]
rs5762139	0.87[ASN][1000 genomes]
rs6005422	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6005423	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005427	0.95[ASN][1000 genomes]
rs73427534	0.95[ASN][1000 genomes]
rs79557	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv834167	chr22:27758395-27910985	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv459864	chr22:27760086-27865344	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv588875	chr22:27760086-27865344	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27812600-27816800	Enhancers	HUVEC	blood vessel
2	chr22:27812600-27817000	Enhancers	NH-A	brain
3	chr22:27812600-27817800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr22:27812800-27816600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr22:27812800-27817400	Weak transcription	Fetal Thymus	thymus
6	chr22:27813000-27816200	Weak transcription	Right Atrium	heart
7	chr22:27813200-27816400	Weak transcription	NHLF	lung
8	chr22:27813400-27816400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr22:27813400-27816400	Weak transcription	Ovary	ovary
10	chr22:27813600-27816400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr22:27813600-27816400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr22:27813800-27816400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr22:27813800-27816400	Weak transcription	Fetal Lung	lung
14	chr22:27813800-27816400	Weak transcription	NHDF-Ad	bronchial
15	chr22:27813800-27816800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr22:27813800-27817200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr22:27813800-27817400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr22:27813800-27817600	Enhancers	Brain Germinal Matrix	brain
19	chr22:27814000-27816200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr22:27814000-27816400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr22:27814000-27816400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr22:27814000-27816600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr22:27814000-27816800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr22:27814000-27817000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr22:27814200-27816400	Weak transcription	Gastric	stomach
26	chr22:27814200-27816600	Weak transcription	Fetal Brain Female	brain
27	chr22:27814200-27816800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr22:27814200-27817800	Enhancers	Pancreas	Pancrea
29	chr22:27814400-27816800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr22:27814600-27816400	Weak transcription	Fetal Brain Male	brain
31	chr22:27814600-27817600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr22:27814800-27816600	Enhancers	NHEK	skin
33	chr22:27814800-27816800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr22:27814800-27816800	Enhancers	HMEC	breast
35	chr22:27814800-27817400	Enhancers	Brain Hippocampus Middle	brain
36	chr22:27814800-27817400	Enhancers	Brain Substantia Nigra	brain
37	chr22:27815200-27816400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr22:27815200-27816800	Enhancers	HSMM	muscle
39	chr22:27815200-27817000	Enhancers	Brain Angular Gyrus	brain
40	chr22:27815200-27817400	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr22:27815400-27817200	Enhancers	Brain Cingulate Gyrus	brain
42	chr22:27815400-27817400	Enhancers	Liver	Liver
43	chr22:27815600-27816400	Weak transcription	Colon Smooth Muscle	Colon
44	chr22:27815600-27816800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr22:27815600-27817400	Enhancers	Brain Anterior Caudate	brain
46	chr22:27815600-27817600	Enhancers	Fetal Kidney	kidney
47	chr22:27815600-27818000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr22:27815800-27816200	Weak transcription	Fetal Stomach	stomach
49	chr22:27815800-27816200	Weak transcription	HSMMtube	muscle

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