Variant report

Variant	rs2842459
Chromosome Location	chr6:76015561-76015562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1018471	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10806035	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10943241	0.81[CHB][hapmap]
rs171263	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2250989	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240374	1.00[YRI][hapmap]
rs240375	0.84[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240378	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs240379	0.89[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240380	0.88[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2748252	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2808203	0.81[CHB][hapmap]
rs2842445	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842446	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842458	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842462	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842463	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4275021	0.88[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4295446	0.83[ASN][1000 genomes]
rs4374801	0.85[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4412169	0.83[AMR][1000 genomes]
rs4541712	0.82[CHB][hapmap]
rs4568415	0.82[CHB][hapmap]
rs4708179	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4708181	0.81[CHB][hapmap]
rs6903526	0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs6904580	0.81[CHB][hapmap]
rs6913979	0.81[CHB][hapmap]
rs6929270	0.84[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7451911	0.81[CHB][hapmap]
rs7743227	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7766441	0.81[CHB][hapmap]
rs7771904	0.81[CHB][hapmap]
rs7772989	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs9341514	0.81[CHB][hapmap]
rs9341515	0.81[AMR][1000 genomes]
rs9343283	0.83[EUR][1000 genomes]
rs9352202	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9359122	0.81[CHB][hapmap]
rs9443171	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer 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
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats 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	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2842459	HMGB1P39	cis	Nerve Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75995200-76016800	Weak transcription	Left Ventricle	heart
2	chr6:75995400-76021800	Weak transcription	Right Ventricle	heart
3	chr6:75995400-76027600	Weak transcription	Aorta	Aorta
4	chr6:75995800-76018200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:75995800-76027200	Weak transcription	Fetal Stomach	stomach
6	chr6:75996000-76022600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:76010200-76016000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:76010200-76018400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:76010200-76019800	Weak transcription	Lung	lung
10	chr6:76010200-76021800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:76010200-76021800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:76010200-76027400	Weak transcription	Psoas Muscle	Psoas
13	chr6:76010400-76015600	Weak transcription	HUVEC	blood vessel
14	chr6:76010400-76027600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:76011200-76017200	Weak transcription	HSMMtube	muscle
16	chr6:76012400-76022200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:76014200-76019800	Weak transcription	Right Atrium	heart
18	chr6:76014800-76016600	Enhancers	Fetal Lung	lung
19	chr6:76014800-76019000	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:76015200-76016200	Enhancers	Colon Smooth Muscle	Colon
21	chr6:76015200-76016400	Enhancers	Fetal Heart	heart
22	chr6:76015400-76016200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:76015400-76016200	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links