Variant report

Variant	rs12546479
Chromosome Location	chr8:103897121-103897122
allele	A/G
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:103892215..103893927-chr8:103895806..103898464,2	K562	blood:
2	chr8:103890973..103894379-chr8:103896304..103898510,3	MCF-7	breast:
3	chr8:103877044..103878892-chr8:103894201..103897134,2	K562	blood:
4	chr8:103874979..103878082-chr8:103895307..103897449,3	MCF-7	breast:
5	chr8:103873112..103878892-chr8:103892937..103898516,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLF10-1	chr8:103895319-103899375	XLOC_007173

No data

Variant related genes	Relation type
ENSG00000253320	Chromatin interaction
ENSG00000155096	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12544232	0.86[AMR][1000 genomes]
rs12546636	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12546960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12547652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12548745	1.00[CHB][hapmap]
rs12549011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12549073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12550185	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533182	1.00[CHB][hapmap]
rs17197341	0.89[AMR][1000 genomes]
rs17197736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17198079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17775390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2137339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734673	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734676	0.86[AMR][1000 genomes]
rs4734678	0.86[AMR][1000 genomes]
rs4734680	1.00[CHB][hapmap]
rs56854051	0.84[AMR][1000 genomes]
rs62522573	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62522576	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522623	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62526529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62526533	0.83[AMR][1000 genomes]
rs62526534	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1021898	chr8:103767324-103922482	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv891245	chr8:103838004-103907253	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103877000-103906800	Weak transcription	Gastric	stomach
2	chr8:103877800-103902000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr8:103877800-103906400	Weak transcription	HSMMtube	muscle
4	chr8:103878000-103906400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr8:103878000-103908800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr8:103878200-103897400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr8:103878200-103906600	Weak transcription	Ovary	ovary
8	chr8:103878400-103897200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr8:103878600-103897600	Weak transcription	Fetal Brain Female	brain
10	chr8:103878800-103899800	Weak transcription	Esophagus	oesophagus
11	chr8:103879200-103922000	Weak transcription	Fetal Intestine Small	intestine
12	chr8:103881000-103899000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr8:103882800-103906600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr8:103884400-103900600	Weak transcription	Aorta	Aorta
15	chr8:103884600-103897400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr8:103886800-103898800	Weak transcription	Fetal Thymus	thymus
17	chr8:103889800-103899000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr8:103889800-103906200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr8:103889800-103906400	Weak transcription	Brain Substantia Nigra	brain
20	chr8:103890000-103899000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr8:103890000-103906400	Weak transcription	Brain Hippocampus Middle	brain
22	chr8:103890000-103906600	Weak transcription	Brain Anterior Caudate	brain
23	chr8:103890000-103906600	Weak transcription	Right Ventricle	heart
24	chr8:103890200-103900400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr8:103890200-103906400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr8:103891000-103899000	Weak transcription	Spleen	Spleen
27	chr8:103891000-103906600	Weak transcription	Liver	Liver
28	chr8:103891400-103897400	Weak transcription	Adipose Nuclei	Adipose
29	chr8:103891800-103907200	Weak transcription	Brain Germinal Matrix	brain
30	chr8:103893200-103902200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr8:103893600-103906800	Weak transcription	Left Ventricle	heart
32	chr8:103893600-103906800	Weak transcription	Pancreas	Pancrea
33	chr8:103893800-103900600	Weak transcription	Lung	lung
34	chr8:103894000-103906400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr8:103894000-103906600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr8:103894200-103906000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr8:103894200-103906200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr8:103894200-103906600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr8:103894200-103914600	Weak transcription	Fetal Lung	lung
40	chr8:103894800-103902200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr8:103895400-103898800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr8:103895800-103898800	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr8:103895800-103901000	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr8:103896000-103897200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr8:103896000-103906200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr8:103896000-103906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr8:103896200-103898800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr8:103896400-103899000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr8:103896400-103911200	Weak transcription	Primary T cells from cord blood	blood
50	chr8:103896600-103898600	Flanking Active TSS	GM12878-XiMat	blood

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