Variant report

Variant	rs6048804
Chromosome Location	chr20:23439967-23439968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr20:23439759-23440051	GM12878	blood:	n/a	chr20:23439887-23439898 chr20:23439888-23439897 chr20:23439888-23439897 chr20:23439886-23439899
2	ZNF143	chr20:23439956-23440031	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZNF143	chr20:23439917-23440003	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23435629..23437264-chr20:23438674..23441153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200208	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12329513	0.82[AFR][1000 genomes]
rs12329580	0.82[AFR][1000 genomes]
rs12329581	0.82[AFR][1000 genomes]
rs12329582	0.82[AFR][1000 genomes]
rs12329588	0.82[AFR][1000 genomes]
rs12329592	0.82[AFR][1000 genomes]
rs6036416	0.82[AFR][1000 genomes]
rs6036417	0.82[AFR][1000 genomes]
rs6036419	0.82[AFR][1000 genomes]
rs6048805	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6048806	1.00[AMR][1000 genomes]
rs6106657	0.82[AFR][1000 genomes]
rs6106661	0.82[AFR][1000 genomes]
rs6106664	0.82[AFR][1000 genomes]
rs6106665	0.82[AFR][1000 genomes]
rs6106666	0.83[YRI][hapmap]
rs6114104	0.82[AFR][1000 genomes]
rs6114105	0.82[AFR][1000 genomes]
rs6114107	0.82[AFR][1000 genomes]
rs6114111	0.82[AFR][1000 genomes]
rs6114112	0.82[AFR][1000 genomes]
rs6114113	0.82[AFR][1000 genomes]
rs6114115	0.82[AFR][1000 genomes]
rs6114116	0.82[AFR][1000 genomes]
rs6114117	0.82[AFR][1000 genomes]
rs6114122	0.82[AFR][1000 genomes]
rs6114123	0.82[AFR][1000 genomes]
rs6114124	0.82[AFR][1000 genomes]
rs6114125	0.82[AFR][1000 genomes]
rs6114127	0.86[AFR][1000 genomes]
rs6114131	0.82[AFR][1000 genomes]
rs6114132	0.82[AFR][1000 genomes]
rs6114133	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv979404	chr20:23429655-23455778	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23417800-23441000	Weak transcription	Right Atrium	heart
2	chr20:23432600-23446000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr20:23434000-23440400	Enhancers	Fetal Thymus	thymus
4	chr20:23434800-23445200	Weak transcription	Esophagus	oesophagus
5	chr20:23436400-23441000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr20:23437400-23440600	Weak transcription	Fetal Muscle Leg	muscle
7	chr20:23437400-23441000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr20:23438600-23440400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr20:23439400-23445000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr20:23439600-23440800	Enhancers	HSMMtube	muscle
11	chr20:23439800-23440600	Enhancers	Fetal Stomach	stomach

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