Variant report

Variant	rs405409
Chromosome Location	chr1:76082628-76082629
allele	G/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76073216..76076150-chr1:76081319..76083961,2	MCF-7	breast:
2	chr1:76081387..76082907-chr17:41398843..41400712,2	K562	blood:
3	chr1:76079907..76082887-chr11:62607623..62609125,2	K562	blood:
4	chr1:75984267..75985784-chr1:76081741..76084002,2	K562	blood:
5	chr1:76081802..76083861-chr1:76085137..76086923,2	K562	blood:
6	chr1:76080604..76083289-chr1:76094142..76096069,2	K562	blood:
7	chr1:76079906..76082887-chr11:62607618..62609123,2	K562	blood:
8	chr1:76081387..76082907-chr17:41398843..41401870,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1265895	0.84[EUR][1000 genomes]
rs169830	0.87[EUR][1000 genomes]
rs169831	0.84[EUR][1000 genomes]
rs1739901	0.84[EUR][1000 genomes]
rs190026	0.82[EUR][1000 genomes]
rs211677	0.87[EUR][1000 genomes]
rs211680	0.87[EUR][1000 genomes]
rs211697	0.87[EUR][1000 genomes]
rs211698	0.82[EUR][1000 genomes]
rs211701	0.87[EUR][1000 genomes]
rs211704	0.87[EUR][1000 genomes]
rs211741	0.82[EUR][1000 genomes]
rs211742	0.87[EUR][1000 genomes]
rs211743	0.87[EUR][1000 genomes]
rs211760	0.87[EUR][1000 genomes]
rs211761	0.87[EUR][1000 genomes]
rs211763	0.82[EUR][1000 genomes]
rs211765	0.82[EUR][1000 genomes]
rs211766	0.87[EUR][1000 genomes]
rs211767	0.82[EUR][1000 genomes]
rs378926	0.87[EUR][1000 genomes]
rs388870	0.87[EUR][1000 genomes]
rs408340	0.87[EUR][1000 genomes]
rs431959	0.87[EUR][1000 genomes]
rs6593582	0.87[EUR][1000 genomes]
rs9324206	0.93[EUR][1000 genomes];1.00[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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv3445096	chr1:75933216-76126980	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv427675	chr1:76070382-76187748	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv10284	chr1:76079955-76082780	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76080000-76082800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
2	chr1:76080000-76082800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:76080200-76082800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:76080200-76083000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:76080400-76082800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:76080600-76082800	Active TSS	Brain Angular Gyrus	brain
7	chr1:76080600-76082800	Active TSS	Brain Cingulate Gyrus	brain
8	chr1:76081000-76082800	Enhancers	Lung	lung
9	chr1:76081000-76083000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr1:76081600-76082800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr1:76081600-76082800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
12	chr1:76082000-76082800	Bivalent Enhancer	Liver	Liver
13	chr1:76082200-76082800	Bivalent Enhancer	Adipose Nuclei	Adipose
14	chr1:76082200-76083000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:76082200-76083000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr1:76082200-76083000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
17	chr1:76082400-76082800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:76082400-76082800	Active TSS	Fetal Brain Female	brain
19	chr1:76082400-76082800	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr1:76082400-76082800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
21	chr1:76082400-76083000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
22	chr1:76082400-76083000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:76082400-76083000	Enhancers	K562	blood
24	chr1:76082400-76083200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
25	chr1:76082600-76082800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:76082600-76082800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr1:76082600-76082800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr1:76082600-76082800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:76082600-76082800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:76082600-76082800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
31	chr1:76082600-76082800	Enhancers	Brain Hippocampus Middle	brain
32	chr1:76082600-76082800	Enhancers	Colon Smooth Muscle	Colon
33	chr1:76082600-76082800	Enhancers	Fetal Brain Male	brain
34	chr1:76082600-76082800	Bivalent Enhancer	Fetal Heart	heart
35	chr1:76082600-76082800	Bivalent Enhancer	Fetal Stomach	stomach
36	chr1:76082600-76082800	Enhancers	Ovary	ovary
37	chr1:76082600-76082800	Enhancers	Stomach Smooth Muscle	stomach
38	chr1:76082600-76083000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:76082600-76083000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:76082600-76083000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:76082600-76083000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:76082600-76083000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:76082600-76083000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr1:76082600-76083000	Bivalent Enhancer	HUVEC	blood vessel
45	chr1:76082600-76085200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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