Variant report

Variant	rs9526582
Chromosome Location	chr13:50207220-50207221
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50205655..50207787-chr13:50213059..50215226,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1359541	0.82[JPT][hapmap]
rs1535467	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925743	0.93[ASN][1000 genomes]
rs3803185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3969	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4415919	0.84[ASN][1000 genomes]
rs4942851	0.82[JPT][hapmap]
rs4942859	0.94[JPT][hapmap]
rs7322886	0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7322971	0.84[ASW][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.91[YRI][hapmap]
rs7981043	0.92[ASN][1000 genomes]
rs9526580	0.82[JPT][hapmap]
rs9535267	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9535277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9526582	ARL11	Cis_1M	lymphoblastoid	RTeQTL
rs9526582	RNASEH2B	cis	parietal	SCAN
rs9526582	ESD	cis	cerebellum	SCAN
rs9526582	RCBTB1	cis	cerebellum	SCAN
rs9526582	CAB39L	cis	cerebellum	SCAN
rs9526582	RCBTB1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50200400-50209800	Weak transcription	Gastric	stomach
2	chr13:50202400-50210000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:50202800-50233600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:50203000-50209000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr13:50203000-50209000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr13:50203000-50209400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr13:50203200-50208800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr13:50203200-50209000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:50203200-50210600	Weak transcription	Small Intestine	intestine
10	chr13:50203200-50212200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr13:50203400-50209200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr13:50203600-50209800	Weak transcription	Primary T cells from cord blood	blood
13	chr13:50204000-50209200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:50204000-50209200	Weak transcription	Right Atrium	heart
15	chr13:50204000-50209800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr13:50204200-50209200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr13:50204200-50209200	Weak transcription	Right Ventricle	heart
18	chr13:50204600-50209000	Weak transcription	GM12878-XiMat	blood
19	chr13:50204600-50210000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr13:50204800-50208400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr13:50205000-50207400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr13:50205200-50208800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr13:50205200-50209200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr13:50205200-50209200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr13:50205200-50209400	Weak transcription	Thymus	Thymus
26	chr13:50205200-50215400	Weak transcription	Esophagus	oesophagus
27	chr13:50205400-50209000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr13:50205400-50209000	Weak transcription	Fetal Thymus	thymus
29	chr13:50205400-50210000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr13:50205800-50210800	Enhancers	Fetal Heart	heart
31	chr13:50206000-50209200	Weak transcription	Fetal Intestine Small	intestine
32	chr13:50206000-50209400	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr13:50206000-50211200	Genic enhancers	Primary B cells from cord blood	blood
34	chr13:50206200-50209000	Weak transcription	Lung	lung
35	chr13:50206200-50209200	Weak transcription	Spleen	Spleen
36	chr13:50206800-50207400	Enhancers	K562	blood
37	chr13:50206800-50208000	Enhancers	Left Ventricle	heart
38	chr13:50206800-50209200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr13:50206800-50209800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr13:50207000-50208800	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr13:50207200-50208400	Enhancers	HUVEC	blood vessel
42	chr13:50207200-50208800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr13:50207200-50209000	Weak transcription	Primary B cells from peripheral blood	blood

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