Variant report

Variant	rs1543525
Chromosome Location	chr13:52388765-52388766
allele	C/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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr13:52374427..52380555-chr13:52387086..52391599,9	MCF-7	breast:
2	chr13:52387525..52389920-chr13:52398590..52400891,3	K562	blood:
3	chr13:52387973..52389920-chr13:52398590..52400891,2	K562	blood:
4	chr13:52388590..52390745-chr13:52574163..52575780,2	MCF-7	breast:
5	chr13:52378339..52383117-chr13:52386356..52389758,6	K562	blood:
6	chr13:52024750..52029081-chr13:52386237..52389081,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHRS12-1	chr13:52387483-52391249	ENSG00000246013

No data

Variant related genes	Relation type
ENSG00000224892	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000231856	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1923875	0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[ASN][1000 genomes]
rs7992588	0.95[JPT][hapmap]
rs9535762	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap];0.95[ASN][1000 genomes]
rs9535763	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9535765	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs975504	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv1840020	chr13:52345838-52388765	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1543525	C13orf1	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52378600-52389200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr13:52379000-52389000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:52379000-52389200	Weak transcription	Ovary	ovary
4	chr13:52379400-52389000	Weak transcription	Placenta	Placenta
5	chr13:52379400-52389200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr13:52379600-52389000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr13:52379600-52389000	Weak transcription	Fetal Intestine Small	intestine
8	chr13:52379600-52389000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr13:52379600-52389200	Weak transcription	Thymus	Thymus
10	chr13:52379800-52389200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr13:52379800-52389200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr13:52379800-52392200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr13:52379800-52392200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr13:52380000-52389000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr13:52380200-52388800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr13:52380200-52389000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr13:52380200-52393200	Weak transcription	Aorta	Aorta
18	chr13:52380800-52389200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr13:52381200-52389000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr13:52382000-52388800	Weak transcription	Pancreas	Pancrea
21	chr13:52382200-52389000	Weak transcription	Right Atrium	heart
22	chr13:52383400-52389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr13:52384200-52389000	Weak transcription	Esophagus	oesophagus
24	chr13:52384600-52389000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr13:52385200-52389000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr13:52385200-52389200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr13:52385400-52388800	Weak transcription	Fetal Thymus	thymus
28	chr13:52385400-52393200	Weak transcription	Spleen	Spleen
29	chr13:52385600-52389000	Weak transcription	Dnd41	blood
30	chr13:52385800-52389000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr13:52386200-52389000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:52386400-52389000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr13:52386400-52389000	Weak transcription	Adipose Nuclei	Adipose
34	chr13:52386400-52389000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr13:52386400-52389000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr13:52386400-52389000	Weak transcription	Left Ventricle	heart
37	chr13:52386400-52389000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr13:52386400-52389000	Weak transcription	HUVEC	blood vessel
39	chr13:52386400-52393200	Weak transcription	Lung	lung
40	chr13:52386600-52388800	Weak transcription	A549	lung
41	chr13:52386600-52388800	Weak transcription	Hela-S3	cervix
42	chr13:52386600-52389000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr13:52386600-52389000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr13:52386600-52389000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr13:52386600-52389000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr13:52386600-52389000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr13:52386600-52389000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr13:52386600-52389000	Weak transcription	K562	blood
49	chr13:52386600-52389200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr13:52386600-52389200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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