Variant report

Variant	rs4960047
Chromosome Location	chr6:4908287-4908288
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	chr6:4907717..4910185-chr6:4913859..4916843,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1113341	0.91[EUR][1000 genomes]
rs1891046	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3930304	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4144546	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4960049	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62384663	0.82[ASN][1000 genomes]
rs62384665	0.95[ASN][1000 genomes]
rs6904931	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7738275	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7738459	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7739834	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7742807	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7759221	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7770206	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7771387	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9378917	0.87[ASN][1000 genomes]
rs9378918	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9378920	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9392068	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4882800-4909000	Weak transcription	Brain Anterior Caudate	brain
2	chr6:4890600-4913800	Weak transcription	Hela-S3	cervix
3	chr6:4893200-4912600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:4893400-4909000	Weak transcription	Brain Angular Gyrus	brain
5	chr6:4893600-4910200	Weak transcription	Esophagus	oesophagus
6	chr6:4893600-4914000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:4895000-4917000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:4895200-4909000	Weak transcription	Adipose Nuclei	Adipose
9	chr6:4898800-4910200	Weak transcription	Psoas Muscle	Psoas
10	chr6:4899000-4909000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:4899200-4913000	Weak transcription	Ovary	ovary
12	chr6:4900000-4913600	Weak transcription	Brain Substantia Nigra	brain
13	chr6:4900200-4915200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:4900200-4918800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:4901600-4913400	Strong transcription	Fetal Stomach	stomach
16	chr6:4902000-4918400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:4902400-4910000	Weak transcription	Pancreas	Pancrea
18	chr6:4902400-4910200	Weak transcription	Liver	Liver
19	chr6:4903400-4912600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:4904200-4913800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:4904200-4914400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:4904400-4909000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr6:4904800-4910600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:4905000-4909000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:4905000-4909400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr6:4905200-4908600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:4905200-4909000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:4905400-4912800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:4905600-4910400	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:4905800-4908400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr6:4905800-4908400	Weak transcription	Right Ventricle	heart
32	chr6:4905800-4931200	Weak transcription	HepG2	liver
33	chr6:4906000-4908600	Enhancers	Primary B cells from peripheral blood	blood
34	chr6:4906200-4908600	Flanking Active TSS	GM12878-XiMat	blood
35	chr6:4906400-4908600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr6:4906400-4908800	Enhancers	Fetal Thymus	thymus
37	chr6:4906400-4911000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:4906400-4911000	Enhancers	Stomach Mucosa	stomach
39	chr6:4906600-4908400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:4906600-4908600	Enhancers	Left Ventricle	heart
41	chr6:4906600-4908600	Enhancers	Right Atrium	heart
42	chr6:4906600-4908800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:4906600-4908800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:4906600-4910800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:4906800-4912000	Weak transcription	Fetal Brain Female	brain
46	chr6:4906800-4913400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:4906800-4914000	Weak transcription	Fetal Kidney	kidney
48	chr6:4907000-4908400	Enhancers	NHDF-Ad	bronchial
49	chr6:4907000-4909000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:4907000-4909000	Weak transcription	A549	lung

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