Variant report

Variant	rs11962460
Chromosome Location	chr6:3991150-3991151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:3942356..3944473-chr6:3989662..3991254,2	MCF-7	breast:
2	chr6:3748250..3749119-chr6:3990628..3991635,6	MCF-7	breast:
3	chr6:3849386..3850175-chr6:3990775..3991654,3	MCF-7	breast:
4	chr6:3742358..3743291-chr6:3990794..3991716,5	K562	blood:
5	chr6:3990717..3994898-chr6:4017557..4021818,5	MCF-7	breast:
6	chr6:3748347..3748962-chr6:3990798..3991690,2	K562	blood:
7	chr6:3848965..3850055-chr6:3990764..3991325,3	K562	blood:
8	chr6:3741878..3742970-chr6:3990744..3991611,4	MCF-7	breast:
9	chr6:3849415..3850026-chr6:3990782..3991740,2	MCF-7	breast:
10	chr6:3279560..3280469-chr6:3990998..3991711,3	K562	blood:
11	chr6:3985295..3987675-chr6:3989539..3991361,2	MCF-7	breast:
12	chr6:3988050..3991356-chr6:3993338..3995417,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000112739	Chromatin interaction
ENSG00000145945	Chromatin interaction
ENSG00000272248	Chromatin interaction
ENSG00000230648	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11242896	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12216086	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1324450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3761786	0.82[AMR][1000 genomes]
rs4266528	0.92[JPT][hapmap]
rs4959921	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs58275491	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs644150	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs654954	1.00[CEU][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes]
rs664264	1.00[CEU][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes]
rs6912179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6931794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6934443	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6937619	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6938648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs723796	0.92[JPT][hapmap]
rs73721499	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73721501	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9392545	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9392549	0.85[AMR][1000 genomes]
rs9405695	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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 target site	56 gene(s)	inside rSNPs	diseases
4	esv1800199	chr6:3986611-4014872	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3979000-4003200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr6:3980600-4003600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:3985400-4011000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:3987800-3993200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:3987800-3997200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:3987800-3998800	Weak transcription	Primary T cells from cord blood	blood
7	chr6:3988200-3997000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:3988400-3991200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:3988400-3991400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:3990400-3991400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:3990600-3991200	Active TSS	Colon Smooth Muscle	Colon
12	chr6:3990600-3991200	Active TSS	Right Atrium	heart
13	chr6:3990600-3991200	Active TSS	Osteobl	bone
14	chr6:3990600-3991400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:3990600-3991400	Enhancers	Fetal Brain Male	brain
16	chr6:3990600-3991800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:3990600-3991800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:3990800-3991200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:3990800-3991200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:3990800-3991200	Active TSS	Brain Cingulate Gyrus	brain
21	chr6:3990800-3991200	Active TSS	Brain Hippocampus Middle	brain
22	chr6:3990800-3991200	Flanking Active TSS	Esophagus	oesophagus
23	chr6:3990800-3991200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr6:3990800-3991200	Active TSS	Left Ventricle	heart
25	chr6:3990800-3991200	Flanking Active TSS	Ovary	ovary
26	chr6:3990800-3991200	Flanking Active TSS	Pancreas	Pancrea
27	chr6:3990800-3991200	Active TSS	Psoas Muscle	Psoas
28	chr6:3990800-3991200	Active TSS	Rectal Smooth Muscle	rectum
29	chr6:3990800-3991200	Active TSS	Right Ventricle	heart
30	chr6:3990800-3991400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:3990800-3991400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:3990800-3991400	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr6:3990800-3991400	Active TSS	Brain Angular Gyrus	brain
34	chr6:3990800-3991400	Active TSS	Brain Anterior Caudate	brain
35	chr6:3990800-3991400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:3990800-3991400	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr6:3990800-3991600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:3990800-3991600	Flanking Active TSS	Placenta	Placenta
39	chr6:3990800-3991600	Flanking Active TSS	HMEC	breast
40	chr6:3990800-3991600	Enhancers	HUVEC	blood vessel
41	chr6:3990800-3991800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr6:3990800-3991800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr6:3990800-3991800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:3990800-3991800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:3990800-3991800	Active TSS	Aorta	Aorta
46	chr6:3990800-3991800	Enhancers	Fetal Muscle Leg	muscle
47	chr6:3990800-3991800	Active TSS	NHDF-Ad	bronchial
48	chr6:3990800-3992000	Enhancers	Fetal Intestine Small	intestine
49	chr6:3990800-3993200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:3991000-3991200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links