Variant report

Variant	rs505688
Chromosome Location	chr11:74495622-74495623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74487704..74490461-chr11:74495466..74498381,2	MCF-7	breast:
2	chr11:74486775..74489120-chr11:74491208..74495917,4	MCF-7	breast:
3	chr11:74494044..74497325-chr11:74499234..74501593,3	K562	blood:
4	chr11:74495037..74497602-chr11:74515702..74517851,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11236269	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11605604	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12363224	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs1282460	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1282461	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1282690	0.86[AMR][1000 genomes]
rs1282692	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs1282695	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1292895	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs1297319	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1303525	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1315297	0.81[AMR][1000 genomes]
rs1583342	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2033532	0.86[ASW][hapmap];0.85[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs41531051	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs471462	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs473080	0.86[AMR][1000 genomes]
rs473256	0.86[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs480840	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs483615	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944945	0.83[LWK][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap]
rs502225	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs508319	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs511890	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs512780	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs513137	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs519741	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs527529	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs529249	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs529488	0.86[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs537054	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs538502	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs543244	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes]
rs546643	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs550491	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs550980	0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs557483	0.84[AMR][1000 genomes]
rs561589	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]
rs565767	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs567956	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs568558	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs568758	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs571446	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs577102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs580142	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs590105	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs599722	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs603062	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs614832	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs624786	0.81[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap]
rs625268	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs629573	0.86[AMR][1000 genomes]
rs641584	0.88[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs643807	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs646287	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs688665	0.82[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs9444	0.92[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs505688	XRRA1	cis	parietal	SCAN
rs505688	XRRA1	cis	cerebellum	SCAN
rs505688	RNF169	cis	multi-tissue	Pritchard
rs505688	FCHSD2	cis	cerebellum	SCAN
rs505688	PLEKHB1	cis	cerebellum	SCAN
rs505688	XRRA1	cis	lymphoblastoid	seeQTL
rs505688	XRRA1	cis	multi-tissue	Pritchard
rs505688	KRTAP5-10	cis	parietal	SCAN
rs505688	RNF169	cis	lymphoblastoid	seeQTL
rs505688	RNF169	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74468000-74500800	Weak transcription	HepG2	liver
2	chr11:74470600-74500800	Weak transcription	Fetal Muscle Leg	muscle
3	chr11:74478000-74501600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:74480200-74501400	Weak transcription	Fetal Intestine Small	intestine
5	chr11:74483800-74497600	Weak transcription	Fetal Heart	heart
6	chr11:74485200-74502600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:74486600-74497800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:74488400-74503800	Weak transcription	Stomach Mucosa	stomach
9	chr11:74488800-74500000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr11:74489800-74500800	Weak transcription	Left Ventricle	heart
11	chr11:74490600-74495800	Weak transcription	Liver	Liver
12	chr11:74490800-74498000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr11:74491000-74496000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:74491000-74496000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr11:74491000-74496000	Enhancers	NHDF-Ad	bronchial
16	chr11:74491400-74495800	Enhancers	Brain Hippocampus Middle	brain
17	chr11:74491600-74496000	Enhancers	Psoas Muscle	Psoas
18	chr11:74491600-74501000	Weak transcription	Fetal Brain Female	brain
19	chr11:74492000-74496200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr11:74492000-74501800	Weak transcription	K562	blood
21	chr11:74492200-74500600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:74492200-74502400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:74492400-74500200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:74492400-74500800	Weak transcription	Placenta	Placenta
25	chr11:74492400-74501000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr11:74492400-74501200	Weak transcription	Fetal Lung	lung
27	chr11:74492800-74496000	Enhancers	Primary B cells from peripheral blood	blood
28	chr11:74492800-74496000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr11:74492800-74496000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:74492800-74496000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr11:74492800-74496200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr11:74493000-74496000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:74493000-74496200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:74493200-74496000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:74493200-74496200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr11:74493400-74496000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:74493400-74496000	Enhancers	HSMM	muscle
38	chr11:74493600-74501400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:74493600-74501600	Weak transcription	Aorta	Aorta
40	chr11:74493800-74495800	Enhancers	Primary hematopoietic stem cells	blood
41	chr11:74493800-74495800	Enhancers	NHLF	lung
42	chr11:74493800-74496000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr11:74494000-74495800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:74494000-74495800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr11:74494000-74496000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:74494000-74496000	Enhancers	Adipose Nuclei	Adipose
47	chr11:74494000-74496000	Enhancers	Brain Cingulate Gyrus	brain
48	chr11:74494000-74496000	Enhancers	Colon Smooth Muscle	Colon
49	chr11:74494000-74496000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr11:74494000-74496000	Enhancers	Rectal Smooth Muscle	rectum

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