Variant report

Variant	rs4290380
Chromosome Location	chr13:52389347-52389348
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:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52381066..52384611-chr13:52388790..52391700,3	MCF-7	breast:
2	chr13:52388956..52389914-chr13:52406314..52407314,7	MCF-7	breast:
3	chr13:52374427..52380555-chr13:52387086..52391599,9	MCF-7	breast:
4	chr13:52387525..52389920-chr13:52398590..52400891,3	K562	blood:
5	chr13:52387973..52389920-chr13:52398590..52400891,2	K562	blood:
6	chr13:52389338..52389872-chr13:52775197..52776130,2	K562	blood:
7	chr13:52389100..52392374-chr13:52395474..52400602,4	MCF-7	breast:
8	chr13:52388590..52390745-chr13:52574163..52575780,2	MCF-7	breast:
9	chr13:52388965..52389862-chr13:52701684..52702477,3	K562	blood:
10	chr13:52378339..52383117-chr13:52386356..52389758,6	K562	blood:
11	chr13:52389093..52389935-chr13:52702977..52703878,2	MCF-7	breast:
12	chr13:52024792..52027224-chr13:52389301..52393113,4	MCF-7	breast:

(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
ENSG00000236778	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000197168	Chromatin interaction
ENSG00000231856	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1034096	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2408526	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7992588	0.83[CEU][hapmap]
rs9316555	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9316556	0.90[EUR][1000 genomes]
rs9526796	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs975504	0.94[CEU][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
rs4290380	C13orf1	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52379800-52392200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:52379800-52392200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr13:52380200-52393200	Weak transcription	Aorta	Aorta
4	chr13:52385400-52393200	Weak transcription	Spleen	Spleen
5	chr13:52386400-52393200	Weak transcription	Lung	lung
6	chr13:52388800-52389800	Flanking Active TSS	GM12878-XiMat	blood
7	chr13:52388800-52389800	Flanking Active TSS	Hela-S3	cervix
8	chr13:52388800-52390400	Enhancers	Fetal Thymus	thymus
9	chr13:52388800-52393400	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr13:52389000-52389400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:52389000-52389400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr13:52389000-52389400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr13:52389000-52389400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr13:52389000-52389400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr13:52389000-52389400	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr13:52389000-52389400	Enhancers	Right Ventricle	heart
17	chr13:52389000-52389400	Active TSS	Stomach Mucosa	stomach
18	chr13:52389000-52389400	Flanking Active TSS	HMEC	breast
19	chr13:52389000-52389600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr13:52389000-52389600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr13:52389000-52389600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr13:52389000-52389600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr13:52389000-52389600	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr13:52389000-52389600	Enhancers	Placenta	Placenta
25	chr13:52389000-52389600	Bivalent/Poised TSS	NHLF	lung
26	chr13:52389000-52389800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr13:52389000-52389800	Enhancers	Primary B cells from peripheral blood	blood
28	chr13:52389000-52389800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr13:52389000-52389800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr13:52389000-52389800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr13:52389000-52389800	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr13:52389000-52389800	Enhancers	Colonic Mucosa	Colon
33	chr13:52389000-52389800	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr13:52389000-52389800	Enhancers	Fetal Muscle Trunk	muscle
35	chr13:52389000-52389800	Enhancers	Psoas Muscle	Psoas
36	chr13:52389000-52389800	Enhancers	Right Atrium	heart
37	chr13:52389000-52389800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr13:52389000-52389800	Flanking Active TSS	HepG2	liver
39	chr13:52389000-52389800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr13:52389000-52390000	Enhancers	Primary hematopoietic stem cells	blood
41	chr13:52389000-52390000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr13:52389000-52390000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr13:52389000-52390000	Flanking Active TSS	Liver	Liver
44	chr13:52389000-52390000	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr13:52389000-52390000	Enhancers	Esophagus	oesophagus
46	chr13:52389000-52390000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr13:52389000-52390000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr13:52389000-52390000	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr13:52389000-52390200	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr13:52389000-52390200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland

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