Variant report

Variant	rs11069825
Chromosome Location	chr13:110761521-110761522
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:110654511..110656415-chr13:110759069..110761693,2	MCF-7	breast:
2	chr13:110443953..110447179-chr13:110758507..110762069,3	MCF-7	breast:
3	chr13:110761020..110763183-chr13:110765963..110768234,2	MCF-7	breast:
4	chr13:110436205..110441713-chr13:110758837..110762777,7	MCF-7	breast:
5	chr13:110760613..110762563-chr13:110777021..110779083,2	MCF-7	breast:
6	chr13:109567424..109568073-chr13:110760960..110761768,2	MCF-7	breast:
7	chr13:110436096..110439350-chr13:110760184..110763012,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185950	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12869698	1.00[ASN][1000 genomes]
rs2218471	1.00[ASN][1000 genomes]
rs2391812	0.80[EUR][1000 genomes]
rs35417370	0.84[EUR][1000 genomes]
rs4238271	1.00[ASN][1000 genomes]
rs56314927	0.85[ASN][1000 genomes]
rs7318126	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988768	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9521601	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv563095	chr13:110724710-110761521	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv901005	chr13:110733102-110766350	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv515849	chr13:110742197-110761521	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv456111	chr13:110742197-110761521	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv456112	chr13:110742197-110761521	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv456113	chr13:110742197-110761521	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv563096	chr13:110742197-110761521	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv563097	chr13:110742197-110766350	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv456114	chr13:110742919-110761521	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv563098	chr13:110742919-110761521	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv901006	chr13:110748857-110806490	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv563099	chr13:110749252-110778894	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv456115	chr13:110756664-110806490	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
14	nsv563100	chr13:110756664-110806490	Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
15	esv3392579	chr13:110758851-110763149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11069825	COL4A2	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110757800-110761600	Weak transcription	Brain Substantia Nigra	brain
2	chr13:110757800-110761600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr13:110758400-110761800	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr13:110759200-110761600	Weak transcription	Right Atrium	heart
5	chr13:110759400-110761600	Weak transcription	Fetal Lung	lung
6	chr13:110759600-110761600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr13:110759600-110762000	Weak transcription	Brain Germinal Matrix	brain
8	chr13:110760000-110762600	Enhancers	Fetal Muscle Trunk	muscle
9	chr13:110760400-110761800	Weak transcription	Fetal Stomach	stomach
10	chr13:110760600-110761600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr13:110760600-110761800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr13:110760800-110761600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr13:110760800-110761600	Enhancers	Lung	lung
14	chr13:110760800-110762800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr13:110760800-110762800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:110760800-110762800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:110760800-110762800	Enhancers	A549	lung
18	chr13:110760800-110763000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr13:110760800-110763000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr13:110760800-110763000	Enhancers	Fetal Heart	heart
21	chr13:110760800-110766400	Weak transcription	Spleen	Spleen
22	chr13:110761000-110761600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr13:110761000-110761600	Enhancers	Adipose Nuclei	Adipose
24	chr13:110761000-110761600	Enhancers	Stomach Smooth Muscle	stomach
25	chr13:110761000-110762000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:110761000-110762000	Flanking Active TSS	Dnd41	blood
27	chr13:110761000-110762000	Enhancers	Hela-S3	cervix
28	chr13:110761000-110762000	Enhancers	NHDF-Ad	bronchial
29	chr13:110761000-110762200	Enhancers	Rectal Smooth Muscle	rectum
30	chr13:110761000-110762600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr13:110761000-110763000	Enhancers	HMEC	breast
32	chr13:110761200-110761600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr13:110761200-110761600	Enhancers	Brain Hippocampus Middle	brain
34	chr13:110761200-110762200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:110761200-110762400	Enhancers	NHEK	skin
36	chr13:110761200-110762800	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr13:110761200-110762800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr13:110761200-110763000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr13:110761200-110763000	Enhancers	Left Ventricle	heart
40	chr13:110761400-110761600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr13:110761400-110761600	Enhancers	HSMM	muscle
42	chr13:110761400-110761800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr13:110761400-110761800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr13:110761400-110761800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr13:110761400-110761800	Enhancers	Placenta	Placenta
46	chr13:110761400-110761800	Enhancers	Right Ventricle	heart
47	chr13:110761400-110762200	Enhancers	Brain Anterior Caudate	brain
48	chr13:110761400-110762600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr13:110761400-110762600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr13:110761400-110762600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links