Variant report

Variant	rs9535528
Chromosome Location	chr13:51489243-51489244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr13:51489095-51489422	GM12878	blood:	n/a	n/a
2	BATF	chr13:51489019-51489289	GM12878	blood:	n/a	n/a
3	BHLHE40	chr13:51489059-51489973	GM12878	blood:	n/a	n/a
4	WRNIP1	chr13:51489187-51489268	GM12878	blood:	n/a	n/a
5	RUNX3	chr13:51488964-51489411	GM12878	blood:	n/a	n/a
6	EP300	chr13:51488759-51489355	K562	blood:	n/a	n/a
7	EP300	chr13:51489019-51489504	GM12878	blood:	n/a	n/a
8	SPI1	chr13:51488983-51489255	GM12891	blood:	n/a	n/a
9	EBF1	chr13:51488918-51489441	GM12878	blood:	n/a	chr13:51489199-51489210
10	EBF1	chr13:51489057-51489290	GM12878	blood:	n/a	chr13:51489199-51489210
11	CHD2	chr13:51489092-51489389	GM12878	blood:	n/a	n/a
12	MTA3	chr13:51488941-51490011	GM12878	blood:	n/a	n/a
13	SPI1	chr13:51489003-51489255	GM12891	blood:	n/a	n/a
14	GATA1	chr13:51488629-51489504	PBDE	blood:	n/a	n/a
15	EBF1	chr13:51488989-51489358	GM12878	blood:	n/a	chr13:51489199-51489210
16	RUNX3	chr13:51488953-51489454	GM12878	blood:	n/a	n/a
17	BATF	chr13:51489059-51489363	GM12878	blood:	n/a	n/a
18	STAT3	chr13:51489017-51489596	GM12878	blood:	n/a	n/a
19	JUND	chr13:51489092-51489376	K562	blood:	n/a	n/a
20	RCOR1	chr13:51488658-51489320	K562	blood:	n/a	n/a
21	SPI1	chr13:51489003-51489313	GM12878	blood:	n/a	n/a
22	ZNF143	chr13:51489021-51489348	GM12878	blood:	n/a	n/a
23	IKZF1	chr13:51488993-51489339	GM12878	blood:	n/a	n/a
24	RCOR1	chr13:51489024-51489292	GM12878	blood:	n/a	n/a
25	FOS	chr13:51489180-51489289	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:51483191..51486510-chr13:51488472..51491289,4	MCF-7	breast:
2	chr13:51488225..51491111-chr13:51497807..51500675,3	K562	blood:
3	chr13:51488232..51490526-chr13:51522667..51525148,2	MCF-7	breast:

Variant related genes	Relation type
RNASEH2B-AS1	TF binding region
ENSG00000136104	Chromatin interaction
ENSG00000233672	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1328360	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17589481	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1870839	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942941	1.00[ASN][1000 genomes]
rs7994724	1.00[ASN][1000 genomes]
rs9526704	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526705	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526708	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535516	1.00[ASN][1000 genomes]
rs9535524	1.00[ASN][1000 genomes]
rs9535525	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535530	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535532	0.89[EUR][1000 genomes]
rs9591369	1.00[ASN][1000 genomes]

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	nsv900077	chr13:51446114-51514831	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9535528	RNASEH2B-AS1	cis	Thyroid	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51485000-51489600	Weak transcription	Spleen	Spleen
2	chr13:51485000-51490800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:51485000-51490800	Weak transcription	Lung	lung
4	chr13:51485000-51491200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:51485000-51496200	Weak transcription	Ovary	ovary
6	chr13:51485200-51495600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr13:51485400-51504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:51485600-51490000	Enhancers	Fetal Heart	heart
9	chr13:51485600-51490600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:51485800-51489400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr13:51485800-51490800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr13:51486000-51489600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr13:51486000-51495800	Weak transcription	Fetal Brain Female	brain
14	chr13:51486200-51490000	Enhancers	NHLF	lung
15	chr13:51486200-51490800	Enhancers	Primary hematopoietic stem cells	blood
16	chr13:51486400-51489400	Weak transcription	Brain Hippocampus Middle	brain
17	chr13:51486400-51490600	Weak transcription	HUVEC	blood vessel
18	chr13:51486400-51490800	Enhancers	Primary B cells from cord blood	blood
19	chr13:51486400-51491000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr13:51486400-51491400	Weak transcription	Brain Substantia Nigra	brain
21	chr13:51486400-51491600	Transcr. at gene 5' and 3'	Dnd41	blood
22	chr13:51486600-51489400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr13:51486600-51489400	Weak transcription	Colonic Mucosa	Colon
24	chr13:51486600-51489400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr13:51486600-51489600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr13:51486600-51489600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr13:51486600-51489800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr13:51486600-51491000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr13:51486600-51491000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr13:51486600-51491200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr13:51486600-51528400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr13:51486800-51489400	Weak transcription	Fetal Intestine Large	intestine
33	chr13:51486800-51489400	Weak transcription	Left Ventricle	heart
34	chr13:51486800-51489400	Weak transcription	Pancreas	Pancrea
35	chr13:51486800-51490400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr13:51486800-51490600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr13:51486800-51490800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr13:51486800-51490800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:51486800-51490800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr13:51486800-51490800	Weak transcription	Brain Anterior Caudate	brain
41	chr13:51486800-51491000	Weak transcription	Fetal Muscle Leg	muscle
42	chr13:51486800-51491200	Weak transcription	Liver	Liver
43	chr13:51486800-51491400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr13:51486800-51491600	Weak transcription	HepG2	liver
45	chr13:51486800-51491800	Weak transcription	Brain Angular Gyrus	brain
46	chr13:51486800-51495600	Weak transcription	Fetal Intestine Small	intestine
47	chr13:51487000-51489400	Weak transcription	Gastric	stomach
48	chr13:51487000-51498400	Weak transcription	Fetal Stomach	stomach
49	chr13:51487200-51490800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr13:51487400-51489400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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