Variant report

Variant	rs975504
Chromosome Location	chr13:52391341-52391342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52381066..52384611-chr13:52388790..52391700,3	MCF-7	breast:
2	chr13:52374427..52380555-chr13:52387086..52391599,9	MCF-7	breast:
3	chr13:52389100..52392374-chr13:52395474..52400602,4	MCF-7	breast:
4	chr13:52390628..52392795-chr13:52410720..52413468,2	MCF-7	breast:
5	chr13:52024792..52027224-chr13:52389301..52393113,4	MCF-7	breast:
6	chr13:52389477..52391775-chr13:52406707..52408443,2	MCF-7	breast:

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

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10220242	0.86[CHB][hapmap]
rs1034096	0.86[EUR][1000 genomes]
rs12584414	0.81[CHB][hapmap]
rs12585859	0.85[CHB][hapmap]
rs1543525	0.95[JPT][hapmap]
rs2408526	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4290380	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]
rs4943028	0.86[CHB][hapmap]
rs621221	0.81[CHB][hapmap]
rs7992588	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs878936	0.86[CHB][hapmap]
rs9316555	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9316556	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526796	1.00[CEU][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes]
rs9535762	0.95[JPT][hapmap]
rs9535763	0.94[JPT][hapmap]
rs9535765	0.94[JPT][hapmap]
rs9591433	0.84[CHB][hapmap]
rs9596586	0.86[CHB][hapmap]
rs9596587	0.82[CHB][hapmap]
rs9634846	0.84[CHB][hapmap]
rs975957	0.83[EUR][1000 genomes];0.99[ASN][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
rs975504	C13orf1	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

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	chr13:52388800-52393400	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr13:52389000-52391400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr13:52389000-52391600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr13:52389000-52394400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr13:52389000-52394600	Enhancers	Fetal Heart	heart
11	chr13:52389200-52391600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr13:52389400-52391600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr13:52389400-52392000	Weak transcription	Right Ventricle	heart
14	chr13:52389600-52393200	Genic enhancers	Primary T cells from cord blood	blood
15	chr13:52389600-52395200	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr13:52389600-52398200	Weak transcription	Brain Substantia Nigra	brain
17	chr13:52389800-52391400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr13:52389800-52391600	Enhancers	Hela-S3	cervix
19	chr13:52389800-52392200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr13:52389800-52392400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr13:52389800-52392600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr13:52389800-52392800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr13:52389800-52393000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr13:52389800-52393000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr13:52389800-52393200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr13:52389800-52393200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr13:52389800-52393200	Weak transcription	Psoas Muscle	Psoas
28	chr13:52389800-52393200	Weak transcription	Right Atrium	heart
29	chr13:52389800-52393800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr13:52389800-52393800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:52389800-52395000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr13:52389800-52395200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr13:52389800-52396000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr13:52389800-52397600	Weak transcription	Brain Hippocampus Middle	brain
35	chr13:52390000-52392600	Weak transcription	GM12878-XiMat	blood
36	chr13:52390000-52393200	Weak transcription	Colon Smooth Muscle	Colon
37	chr13:52390000-52393200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr13:52390000-52393200	Weak transcription	Esophagus	oesophagus
39	chr13:52390000-52393200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr13:52390000-52393200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr13:52390000-52393600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr13:52390000-52393600	Weak transcription	Thymus	Thymus
43	chr13:52390000-52394600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr13:52390000-52394800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr13:52390200-52392000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr13:52390200-52398200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr13:52390400-52392600	Weak transcription	Fetal Thymus	thymus
48	chr13:52390600-52391400	Enhancers	A549	lung
49	chr13:52390600-52392600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr13:52390600-52392800	Weak transcription	Primary B cells from cord blood	blood

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