Variant report

Variant	rs4757473
Chromosome Location	chr11:17013607-17013608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17002569..17005587-chr11:17010572..17013703,3	K562	blood:
2	chr11:17012963..17015420-chr11:17035840..17037615,2	MCF-7	breast:
3	chr11:17011405..17013147-chr11:17013482..17015082,2	MCF-7	breast:
4	chr11:17010780..17015542-chr11:17031310..17035315,5	MCF-7	breast:
5	chr11:17012348..17014489-chr11:17025477..17027730,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166689	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10734250	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs10766366	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10766367	0.91[EUR][1000 genomes]
rs10766370	0.89[YRI][hapmap]
rs10832707	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs10832709	0.96[CEU][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes]
rs10832710	0.96[CEU][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs10832712	0.91[EUR][1000 genomes]
rs10832713	0.80[YRI][hapmap]
rs10832721	0.88[YRI][hapmap]
rs11529141	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468489	0.80[YRI][hapmap]
rs2302207	0.95[CEU][hapmap];0.80[YRI][hapmap];0.91[EUR][1000 genomes]
rs2353369	0.96[CEU][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes]
rs4237715	0.89[EUR][1000 genomes]
rs4237716	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4351794	0.89[YRI][hapmap]
rs4468326	0.86[JPT][hapmap]
rs4469869	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4757468	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757472	0.90[EUR][1000 genomes]
rs4757474	0.91[EUR][1000 genomes]
rs4757475	0.91[EUR][1000 genomes]
rs4757476	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757482	0.80[YRI][hapmap]
rs4757484	0.80[YRI][hapmap]
rs4757490	0.89[YRI][hapmap]
rs6486333	0.89[EUR][1000 genomes]
rs6486334	0.95[CEU][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs6486335	0.80[YRI][hapmap]
rs7118307	0.89[EUR][1000 genomes]
rs7122802	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130826	0.86[JPT][hapmap]
rs7924495	0.86[JPT][hapmap]
rs7931025	0.85[YRI][hapmap]
rs7934567	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940499	0.80[YRI][hapmap]
rs7944490	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4757473	INSC	cis	cerebellum	SCAN
rs4757473	RNU14	cis	multi-tissue	Pritchard

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17004800-17034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:17006400-17034000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:17007000-17014200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:17008200-17014600	Weak transcription	Fetal Lung	lung
5	chr11:17008400-17016000	Weak transcription	Thymus	Thymus
6	chr11:17009200-17015000	Weak transcription	Adipose Nuclei	Adipose
7	chr11:17009400-17014600	Weak transcription	Small Intestine	intestine
8	chr11:17009400-17015800	Weak transcription	Left Ventricle	heart
9	chr11:17009400-17032600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:17009600-17017600	Weak transcription	Ovary	ovary
11	chr11:17009800-17018000	Weak transcription	Spleen	Spleen
12	chr11:17009800-17018800	Weak transcription	A549	lung
13	chr11:17009800-17030000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:17009800-17032600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:17009800-17032600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:17010000-17014400	Weak transcription	Liver	Liver
17	chr11:17010000-17014400	Weak transcription	Fetal Kidney	kidney
18	chr11:17010000-17015600	Weak transcription	Colonic Mucosa	Colon
19	chr11:17010000-17015800	Weak transcription	Lung	lung
20	chr11:17010000-17019000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:17010000-17023000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:17010400-17014200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:17011400-17014000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:17011600-17013800	Strong transcription	Fetal Intestine Large	intestine
25	chr11:17011600-17014600	Weak transcription	Right Ventricle	heart
26	chr11:17011600-17015600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:17011800-17014600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr11:17012200-17014200	Strong transcription	HepG2	liver
29	chr11:17012200-17015000	Weak transcription	Gastric	stomach
30	chr11:17012400-17013800	Weak transcription	Pancreas	Pancrea
31	chr11:17012400-17014200	Strong transcription	Fetal Intestine Small	intestine
32	chr11:17012400-17024200	Enhancers	Stomach Mucosa	stomach
33	chr11:17012600-17017000	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:17013000-17013800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:17013000-17014000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr11:17013000-17014600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:17013200-17013800	Strong transcription	Esophagus	oesophagus
38	chr11:17013200-17013800	Enhancers	Right Atrium	heart
39	chr11:17013400-17014000	Enhancers	Brain Anterior Caudate	brain
40	chr11:17013400-17014000	Strong transcription	Fetal Stomach	stomach
41	chr11:17013400-17016000	Enhancers	Fetal Heart	heart
42	chr11:17013400-17018000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr11:17013400-17033800	Weak transcription	Brain Substantia Nigra	brain
44	chr11:17013600-17014400	Weak transcription	Duodenum Mucosa	Duodenum

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