Variant report

Variant	rs9461478
Chromosome Location	chr6:28757991-28757992
allele	A/C
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28692257..28693945-chr6:28757387..28759135,2	K562	blood:
2	chr6:28677491..28679930-chr6:28756497..28758578,2	K562	blood:
3	chr6:28757752..28760408-chr6:28765977..28767794,2	K562	blood:
4	chr6:28739775..28742884-chr6:28756307..28759477,3	K562	blood:
5	chr6:28752766..28756379-chr6:28756550..28759154,4	K562	blood:
6	chr6:28755863..28758470-chr6:28911484..28913225,2	K562	blood:
7	chr6:28756425..28760621-chr6:28761088..28764506,5	K562	blood:
8	chr6:28665488..28667691-chr6:28756212..28758692,2	K562	blood:
9	chr6:28756573..28759569-chr6:28769791..28772080,4	K562	blood:
10	chr6:28695047..28697144-chr6:28756622..28759292,2	K562	blood:
11	chr6:28725484..28727930-chr6:28757614..28759136,2	K562	blood:
12	chr6:28757312..28759023-chr6:28889870..28891731,2	K562	blood:
13	chr6:28755863..28759570-chr6:28911484..28914475,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204709	Chromatin interaction
ENSG00000265764	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11961493	0.82[EUR][1000 genomes]
rs11963531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964044	0.82[EUR][1000 genomes]
rs11966547	0.82[EUR][1000 genomes]
rs1925764	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131103	0.82[EUR][1000 genomes]
rs34840519	0.82[EUR][1000 genomes]
rs58971829	0.82[EUR][1000 genomes]
rs59858792	0.82[EUR][1000 genomes]
rs6456867	0.82[EUR][1000 genomes]
rs6924860	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73393707	0.82[EUR][1000 genomes]
rs73403168	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs73403179	0.82[EUR][1000 genomes]
rs73403188	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73403189	0.82[EUR][1000 genomes]
rs73407223	0.82[EUR][1000 genomes]
rs73407254	0.82[EUR][1000 genomes]
rs73408589	0.82[EUR][1000 genomes]
rs7739709	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7749527	0.82[EUR][1000 genomes]
rs7762991	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468430	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9501112	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9501420	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28756400-28758600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
2	chr6:28756400-28759200	Active TSS	A549	lung
3	chr6:28756600-28758600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:28756600-28759000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:28756800-28758800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:28756800-28759000	Active TSS	Placenta	Placenta
7	chr6:28756800-28759000	Active TSS	K562	blood
8	chr6:28756800-28759200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:28757000-28758200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:28757000-28758400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:28757000-28758400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:28757000-28758400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:28757200-28758000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
14	chr6:28757200-28758200	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr6:28757200-28758200	Bivalent/Poised TSS	Fetal Brain Female	brain
16	chr6:28757200-28758200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
17	chr6:28757200-28758200	Bivalent/Poised TSS	Fetal Kidney	kidney
18	chr6:28757200-28758400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:28757200-28758400	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
20	chr6:28757200-28758400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
21	chr6:28757200-28758600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:28757200-28758800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:28757200-28759000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr6:28757400-28758000	Bivalent Enhancer	Liver	Liver
25	chr6:28757400-28758000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
26	chr6:28757400-28758000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
27	chr6:28757400-28758000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
28	chr6:28757400-28758000	Bivalent/Poised TSS	Right Atrium	heart
29	chr6:28757400-28758000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
30	chr6:28757400-28758200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:28757400-28758200	Bivalent/Poised TSS	Ovary	ovary
32	chr6:28757400-28758200	Active TSS	HMEC	breast
33	chr6:28757400-28758200	Active TSS	NHEK	skin
34	chr6:28757400-28758400	Bivalent/Poised TSS	HSMM	muscle
35	chr6:28757400-28758600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:28757400-28758600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:28757400-28758600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:28757400-28758600	Active TSS	Osteobl	bone
39	chr6:28757400-28759000	Active TSS	GM12878-XiMat	blood
40	chr6:28757400-28759200	Active TSS	H9 Cell Line	embryonic stem cell
41	chr6:28757600-28758000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:28757600-28758000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:28757600-28758000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:28757600-28758000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
45	chr6:28757600-28758000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
46	chr6:28757600-28758000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
47	chr6:28757600-28758000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
48	chr6:28757600-28758000	Bivalent/Poised TSS	HepG2	liver
49	chr6:28757600-28758000	Active TSS	NH-A	brain
50	chr6:28757600-28758200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links