Variant report

Variant	rs9535762
Chromosome Location	chr13:52390603-52390604
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	chr13:52381066..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	chr13:52388590..52390745-chr13:52574163..52575780,2	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:

(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
ENSG00000231856	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000102796	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1543525	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]
rs1923875	0.85[CHB][hapmap];0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs7992588	0.95[JPT][hapmap]
rs9535763	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535765	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535767	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs9568642	0.82[ASW][hapmap]
rs975504	0.95[JPT][hapmap]

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

No data

Chromatin state (count:74 , 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	chr13:52389000-52391000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr13:52389000-52391000	Enhancers	Left Ventricle	heart
9	chr13:52389000-52391200	Enhancers	K562	blood
10	chr13:52389000-52391400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:52389000-52391600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr13:52389000-52394400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr13:52389000-52394600	Enhancers	Fetal Heart	heart
14	chr13:52389200-52390800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr13:52389200-52391000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:52389200-52391600	Enhancers	Placenta Amnion	Placenta Amnion
17	chr13:52389400-52390800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:52389400-52391600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr13:52389400-52392000	Weak transcription	Right Ventricle	heart
20	chr13:52389600-52390800	Weak transcription	Placenta	Placenta
21	chr13:52389600-52391200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr13:52389600-52393200	Genic enhancers	Primary T cells from cord blood	blood
23	chr13:52389600-52395200	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr13:52389600-52398200	Weak transcription	Brain Substantia Nigra	brain
25	chr13:52389800-52390800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr13:52389800-52390800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr13:52389800-52390800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr13:52389800-52390800	Weak transcription	HMEC	breast
29	chr13:52389800-52391000	Enhancers	Pancreas	Pancrea
30	chr13:52389800-52391200	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr13:52389800-52391400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr13:52389800-52391600	Enhancers	Hela-S3	cervix
33	chr13:52389800-52392200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr13:52389800-52392400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr13:52389800-52392600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr13:52389800-52392800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr13:52389800-52393000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr13:52389800-52393000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr13:52389800-52393200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr13:52389800-52393200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr13:52389800-52393200	Weak transcription	Psoas Muscle	Psoas
42	chr13:52389800-52393200	Weak transcription	Right Atrium	heart
43	chr13:52389800-52393800	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr13:52389800-52393800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr13:52389800-52395000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr13:52389800-52395200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr13:52389800-52396000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr13:52389800-52397600	Weak transcription	Brain Hippocampus Middle	brain
49	chr13:52390000-52390800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr13:52390000-52392600	Weak transcription	GM12878-XiMat	blood

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