Variant report

Variant	rs9349693
Chromosome Location	chr6:53939724-53939725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1325828	0.82[CHB][hapmap]
rs1325831	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1359561	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35307174	0.82[ASN][1000 genomes]
rs4715438	0.86[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs519844	0.82[CHB][hapmap]
rs582710	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs598103	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs614956	0.90[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs625899	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs639665	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs71558041	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9296736	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9370258	0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9370260	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9382280	0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9474720	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs9637973	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv5307	chr6:53874118-53952230	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv603110	chr6:53885918-54103794	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv7901	chr6:53914491-53981080	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv823691	chr6:53918427-53978766	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv885885	chr6:53920024-54046264	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv34853	chr6:53924697-53977449	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1839673	chr6:53927326-53939724	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
12	esv1835741	chr6:53928649-53939724	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
13	nsv603118	chr6:53929484-53939724	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
14	nsv603119	chr6:53929484-53947087	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
15	nsv603120	chr6:53929484-53951857	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv603121	chr6:53929484-53951990	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1017633	chr6:53935336-54118476	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9349693	C6orf142	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53935400-53940600	Weak transcription	Liver	Liver
2	chr6:53935400-53944600	Weak transcription	Right Atrium	heart
3	chr6:53938000-53941000	Weak transcription	Adipose Nuclei	Adipose
4	chr6:53938000-53941000	Weak transcription	Right Ventricle	heart
5	chr6:53938000-53941200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:53938000-53944800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:53938800-53940000	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr6:53939000-53940000	Enhancers	Fetal Muscle Leg	muscle
9	chr6:53939000-53940000	Enhancers	Fetal Stomach	stomach
10	chr6:53939000-53940000	Enhancers	Left Ventricle	heart
11	chr6:53939400-53940000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:53939400-53940000	Enhancers	Ovary	ovary
13	chr6:53939400-53940400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:53939600-53940600	Weak transcription	Fetal Heart	heart
15	chr6:53939600-53941000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:53939600-53941000	Weak transcription	Psoas Muscle	Psoas

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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