Variant report

Variant	rs561589
Chromosome Location	chr11:74532093-74532094
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74526254..74528422-chr11:74532090..74534195,2	MCF-7	breast:
2	chr11:74531301..74533509-chr20:52536139..52539036,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11236269	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11605604	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12363224	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1282460	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1282461	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1282690	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1282692	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1282695	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1292895	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1297319	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1303525	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1315297	0.81[AMR][1000 genomes]
rs1583342	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2033532	0.85[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2919057	0.94[JPT][hapmap]
rs41531051	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs471462	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473080	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs473256	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs480840	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs483615	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4944945	0.83[YRI][hapmap]
rs497772	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs502225	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs505688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs508319	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs511890	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs512780	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513137	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs519741	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs527529	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs529249	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs529488	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs537054	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs538502	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs543244	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs546643	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs550491	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs550980	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs557483	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs565767	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs567956	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs568558	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs568758	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs571446	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs577102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs580142	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs590105	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs599722	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs603062	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs614832	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs624786	0.85[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs625268	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs629573	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs641584	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs643807	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs646287	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs688665	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9444	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs997465	0.94[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	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
7	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv2484083	chr11:74531782-74533314	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs561589	XRRA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74496200-74533000	Weak transcription	Fetal Brain Male	brain
2	chr11:74502800-74545600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:74503000-74533000	Weak transcription	Right Ventricle	heart
4	chr11:74503200-74533000	Weak transcription	Gastric	stomach
5	chr11:74503200-74537800	Weak transcription	Pancreas	Pancrea
6	chr11:74504400-74534600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:74509600-74533000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:74509800-74534600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr11:74515400-74533000	Weak transcription	Esophagus	oesophagus
10	chr11:74519800-74534200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr11:74520000-74533000	Weak transcription	Small Intestine	intestine
12	chr11:74520400-74533200	Strong transcription	Dnd41	blood
13	chr11:74520600-74534400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:74520600-74534800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr11:74520800-74537800	Weak transcription	Colonic Mucosa	Colon
16	chr11:74524800-74535800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:74525400-74534400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:74526400-74534400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr11:74526600-74534000	Strong transcription	Primary B cells from cord blood	blood
20	chr11:74527000-74533000	Weak transcription	Spleen	Spleen
21	chr11:74527200-74534800	Strong transcription	Fetal Intestine Large	intestine
22	chr11:74527400-74533000	Strong transcription	Primary hematopoietic stem cells	blood
23	chr11:74527600-74532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:74527600-74532200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:74527800-74532400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:74527800-74534000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:74527800-74534400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:74527800-74534600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr11:74527800-74534800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:74528000-74532400	Strong transcription	Liver	Liver
31	chr11:74528000-74533000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:74528000-74534000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr11:74528000-74576400	Weak transcription	Stomach Mucosa	stomach
34	chr11:74528200-74534000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:74528400-74533200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr11:74528400-74535000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:74528400-74535600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:74528600-74532200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:74528600-74532400	Strong transcription	Fetal Muscle Leg	muscle
40	chr11:74528600-74533800	Strong transcription	Adipose Nuclei	Adipose
41	chr11:74528800-74533000	Weak transcription	Right Atrium	heart
42	chr11:74528800-74537800	Weak transcription	Lung	lung
43	chr11:74529200-74533000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:74529400-74532200	Genic enhancers	Fetal Stomach	stomach
45	chr11:74529400-74533000	Weak transcription	Aorta	Aorta
46	chr11:74529400-74533000	Weak transcription	Brain Germinal Matrix	brain
47	chr11:74529600-74532200	Enhancers	NHLF	lung
48	chr11:74529800-74532400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr11:74529800-74533000	Weak transcription	Fetal Intestine Small	intestine
50	chr11:74529800-74533800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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