Variant report

Variant	rs1555681
Chromosome Location	chr6:45086367-45086368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1023090	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10948195	0.81[EUR][1000 genomes]
rs10948222	0.88[CEU][hapmap]
rs12204678	0.86[EUR][1000 genomes]
rs12207402	1.00[YRI][hapmap]
rs1324531	0.85[EUR][1000 genomes]
rs1324538	0.86[ASN][1000 genomes]
rs1329713	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs1360196	0.82[EUR][1000 genomes]
rs2038766	0.89[EUR][1000 genomes]
rs2396373	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2396380	0.90[EUR][1000 genomes]
rs2396425	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4373351	0.96[CEU][hapmap]
rs4446571	0.88[CEU][hapmap]
rs6458419	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs6458420	0.88[EUR][1000 genomes]
rs6899845	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs6933553	0.88[EUR][1000 genomes]
rs7451423	0.88[CEU][hapmap]
rs7743116	0.86[EUR][1000 genomes]
rs9296453	0.81[CEU][hapmap]
rs9349315	0.81[EUR][1000 genomes]
rs9357469	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs9357470	0.91[EUR][1000 genomes]
rs9357471	0.88[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357480	0.84[CEU][hapmap]
rs9357484	0.92[CEU][hapmap]
rs9369523	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9369533	0.91[EUR][1000 genomes]
rs9369558	0.88[CEU][hapmap]
rs9381359	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9381366	0.87[EUR][1000 genomes]
rs9381377	0.83[EUR][1000 genomes]
rs9395066	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs9395069	0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9395084	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9395095	0.88[CEU][hapmap]
rs9463078	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9472418	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs976699	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1023018	chr6:44925393-45152912	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538212	chr6:44925393-45152912	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1026728	chr6:45001948-45126730	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv538213	chr6:45001948-45126730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv885865	chr6:45012223-45102025	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv492309	chr6:45020402-45233484	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1032906	chr6:45069368-45212863	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1555681	SUPT3H	cis	multi-tissue	Pritchard
rs1555681	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45083400-45086800	Enhancers	HSMM	muscle
2	chr6:45085400-45087800	Weak transcription	NHDF-Ad	bronchial
3	chr6:45086000-45086400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:45086200-45086400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:45086200-45086400	Enhancers	Fetal Intestine Large	intestine
6	chr6:45086200-45086800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:45086200-45086800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:45086200-45087000	Flanking Active TSS	Fetal Heart	heart
9	chr6:45086200-45087400	Enhancers	Fetal Intestine Small	intestine

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