Variant report

Variant	rs4653906
Chromosome Location	chr1:228314007-228314008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228312167..228314793-chr1:228333464..228337052,3	K562	blood:
2	chr1:228296008..228299455-chr1:228310076..228314109,6	MCF-7	breast:
3	chr1:228309213..228312367-chr1:228313234..228315768,3	K562	blood:
4	chr1:228313411..228315417-chr1:228353319..228355482,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143774	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000162910	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10127705	0.90[EUR][1000 genomes]
rs1034792	0.92[CHB][hapmap]
rs10495278	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10495279	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10916266	0.90[EUR][1000 genomes]
rs1094602	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1094603	0.90[EUR][1000 genomes]
rs11577976	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs11580599	0.86[EUR][1000 genomes]
rs11581037	1.00[CEU][hapmap]
rs11581169	0.90[EUR][1000 genomes]
rs11584418	1.00[CEU][hapmap]
rs11586055	1.00[CEU][hapmap]
rs1188975	0.93[CHB][hapmap]
rs1188977	0.92[CHB][hapmap]
rs12034268	0.86[EUR][1000 genomes]
rs12039801	0.86[EUR][1000 genomes]
rs12088423	1.00[CEU][hapmap]
rs12740965	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1620734	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs1803695	0.90[EUR][1000 genomes]
rs28587961	0.90[EUR][1000 genomes]
rs34687764	0.90[EUR][1000 genomes]
rs3795773	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3795774	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs41303083	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4653533	0.93[CHB][hapmap]
rs4653908	0.86[EUR][1000 genomes]
rs4653909	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653914	0.86[EUR][1000 genomes]
rs61825156	0.90[EUR][1000 genomes]
rs61825157	0.86[EUR][1000 genomes]
rs61825159	0.86[EUR][1000 genomes]
rs61827462	0.86[EUR][1000 genomes]
rs6663726	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6668719	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs708126	0.93[CHB][hapmap]
rs7530253	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7539664	0.92[CHB][hapmap]
rs822727	0.93[CHB][hapmap]
rs860301	0.81[ASN][1000 genomes]
rs9287011	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs9970544	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS 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	187 gene(s)	inside rSNPs	diseases
3	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
5	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228309600-228314200	Enhancers	Fetal Intestine Small	intestine
2	chr1:228309800-228314200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:228313000-228315200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:228313200-228314600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:228313400-228318200	Weak transcription	Fetal Intestine Large	intestine
6	chr1:228313600-228315000	Enhancers	Fetal Stomach	stomach
7	chr1:228313800-228318200	Weak transcription	K562	blood
8	chr1:228314000-228314200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:228314000-228314200	Bivalent Enhancer	NHDF-Ad	bronchial
10	chr1:228314000-228314600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:228314000-228314800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:228314000-228315000	Enhancers	Adipose Nuclei	Adipose

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