Variant report

Variant	rs3004116
Chromosome Location	chr20:23486218-23486219
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1987782	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236085	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983291	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983292	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2983293	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2983294	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983295	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983296	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983297	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983298	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983299	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983300	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983301	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3004100	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3004103	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3004104	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3004105	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3004106	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3004107	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3004108	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3004110	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3004111	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3004112	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3004114	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3004115	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761845	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv912818	chr20:23406519-23567838	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv912819	chr20:23406519-23569400	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv912820	chr20:23406519-23578148	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1065390	chr20:23412890-23569238	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1065719	chr20:23415029-23565333	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv544214	chr20:23415029-23565333	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv470544	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv585722	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv458949	chr20:23426648-23569400	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv585723	chr20:23426648-23569400	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1057992	chr20:23430887-23565333	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv544215	chr20:23430887-23565333	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23471800-23488000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:23484600-23488200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:23486200-23486400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr20:23486200-23486400	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr20:23486200-23487000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr20:23486200-23489600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr20:23486200-23491200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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