Variant report

Variant	rs546576
Chromosome Location	chr2:73501453-73501454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:73501337-73501514	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:73501240..73504099-chr2:73507229..73509023,2	K562	blood:
2	chr2:73460369..73462896-chr2:73500651..73503083,2	K562	blood:
3	chr2:73481859..73485012-chr2:73498373..73502378,4	K562	blood:
4	chr2:73500262..73502727-chr2:73503809..73506884,3	MCF-7	breast:
5	chr2:73499117..73502742-chr2:73504775..73508729,6	K562	blood:
6	chr2:73494870..73498347-chr2:73498508..73505707,9	MCF-7	breast:

No data

Variant related genes	Relation type
FBXO41	TF binding region
ENSG00000135624	Chromatin interaction
ENSG00000163013	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10048837	1.00[JPT][hapmap]
rs10048838	1.00[JPT][hapmap]
rs10175626	1.00[JPT][hapmap]
rs10189022	1.00[JPT][hapmap]
rs11893547	1.00[JPT][hapmap]
rs11902788	1.00[JPT][hapmap]
rs13386236	1.00[JPT][hapmap]
rs13409784	1.00[JPT][hapmap]
rs13415504	1.00[JPT][hapmap]
rs17008829	1.00[JPT][hapmap]
rs17008862	1.00[JPT][hapmap]
rs17008864	1.00[JPT][hapmap]
rs2043092	1.00[JPT][hapmap]
rs2288632	1.00[JPT][hapmap]
rs3820701	1.00[JPT][hapmap]
rs7594590	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013190	chr2:73489679-73572643	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs546576	STAMBP	cis	parietal	SCAN
rs546576	FBXO41	cis	Adipose Subcutaneous	GTEx
rs546576	ALMS1P	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73481800-73510000	Weak transcription	K562	blood
2	chr2:73491200-73504000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr2:73496800-73510400	Weak transcription	Ovary	ovary
4	chr2:73497000-73504000	Weak transcription	Pancreas	Pancrea
5	chr2:73497000-73510000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:73497000-73510200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:73497000-73510400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:73497000-73510400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:73497000-73511000	Weak transcription	Gastric	stomach
10	chr2:73497200-73509800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:73497200-73510200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:73497200-73510200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:73497200-73510200	Weak transcription	Brain Anterior Caudate	brain
14	chr2:73497200-73510200	Weak transcription	Fetal Thymus	thymus
15	chr2:73497200-73510600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:73497400-73504000	Weak transcription	GM12878-XiMat	blood
17	chr2:73497400-73509600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:73497400-73509800	Weak transcription	Hela-S3	cervix
19	chr2:73497400-73510000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:73497400-73510400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:73497400-73510400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:73497400-73511000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:73497600-73510400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:73497600-73510400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:73497800-73510200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:73497800-73510400	Weak transcription	Primary T cells from cord blood	blood
27	chr2:73498000-73510200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:73498400-73510200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr2:73498400-73510200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr2:73498800-73504000	Weak transcription	Primary B cells from cord blood	blood
31	chr2:73499800-73504200	Weak transcription	Dnd41	blood
32	chr2:73499800-73510000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:73499800-73510400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:73500800-73510200	Weak transcription	Spleen	Spleen
35	chr2:73501200-73501600	Strong transcription	HepG2	liver
36	chr2:73501400-73504000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:73501400-73504000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:73501400-73504200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:73501400-73504400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:73501400-73507600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:73501400-73510000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:73501400-73510600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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