Variant report

Variant	rs1477590
Chromosome Location	chr15:56745305-56745306
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11630363	0.93[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11633374	0.86[ASN][1000 genomes]
rs11855094	0.91[CHB][hapmap]
rs12900678	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs12905782	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12908734	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1549452	0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs1554410	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16976890	0.91[CHB][hapmap]
rs1711484	0.83[EUR][1000 genomes]
rs17819438	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2114183	0.87[ASN][1000 genomes]
rs2249090	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs2303441	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2460646	0.85[ASN][1000 genomes]
rs2460650	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs2554287	0.91[CHB][hapmap];0.90[YRI][hapmap]
rs2682054	0.89[CEU][hapmap]
rs2682059	0.85[CEU][hapmap]
rs2713936	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs2718921	0.91[CHB][hapmap]
rs2718934	0.89[CEU][hapmap]
rs2725854	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2725856	0.82[CHB][hapmap];0.90[YRI][hapmap]
rs2947021	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs34755898	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35497167	0.86[ASN][1000 genomes]
rs35863560	0.86[ASN][1000 genomes]
rs3784552	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817406	0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3985758	0.88[ASN][1000 genomes]
rs4774859	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62022122	0.89[ASN][1000 genomes]
rs62022127	0.85[ASN][1000 genomes]
rs62022133	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493856	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs6493858	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7170307	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7174892	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7181235	0.91[CHB][hapmap]
rs7181320	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs795791	0.95[CHB][hapmap]
rs795800	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1545	chr15:56659498-56897381	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1046891	chr15:56659587-56792033	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv471330	chr15:56659709-56896385	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv471506	chr15:56659709-56896385	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv498847	chr15:56667038-56896395	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2525559	chr15:56669294-56897412	Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv433294	chr15:56676457-56853535	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3693203	chr15:56676457-56894478	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv35150	chr15:56677730-56896304	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv9270	chr15:56686946-56760420	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv2757602	chr15:56736478-56790080	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv2760033	chr15:56736478-56790080	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1477590	TEX9	Cis_1M	lymphoblastoid	RTeQTL
rs1477590	FLJ12994	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56716000-56756600	Weak transcription	HSMM	muscle
2	chr15:56718600-56756200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:56722800-56746800	Weak transcription	Thymus	Thymus
4	chr15:56723400-56756600	Weak transcription	Fetal Stomach	stomach
5	chr15:56732200-56756800	Weak transcription	Fetal Brain Male	brain
6	chr15:56734800-56751200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:56735200-56756400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:56735400-56756600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:56735600-56756400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:56735600-56756600	Weak transcription	Brain Anterior Caudate	brain
11	chr15:56736000-56751200	Weak transcription	Fetal Thymus	thymus
12	chr15:56736400-56755200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:56736800-56754400	Weak transcription	Fetal Kidney	kidney
14	chr15:56738400-56756200	Weak transcription	Fetal Lung	lung
15	chr15:56739600-56756600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:56743200-56756800	Weak transcription	Aorta	Aorta
17	chr15:56744600-56751600	Weak transcription	Dnd41	blood
18	chr15:56744600-56757200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links