Variant report

Variant	rs3741414
Chromosome Location	chr12:57844049-57844050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57842276..57845033-chr12:57882153..57884976,2	K562	blood:
2	chr12:57821945..57826454-chr12:57843844..57847049,4	K562	blood:
3	chr12:57841988..57844385-chr12:57912875..57915814,2	K562	blood:
4	chr12:57840047..57842251-chr12:57842325..57845247,2	K562	blood:
5	chr12:57818076..57819912-chr12:57842530..57844475,2	MCF-7	breast:
6	chr12:57821945..57831494-chr12:57839441..57852842,32	K562	blood:
7	chr12:57843448..57846710-chr12:57847033..57851571,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175189	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000208028	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1106766	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11172134	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs11172147	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs11172181	0.86[EUR][1000 genomes]
rs11609805	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11613352	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11614506	0.95[CEU][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12313306	0.81[EUR][1000 genomes]
rs12315434	0.83[EUR][1000 genomes]
rs2122982	0.88[EUR][1000 genomes]
rs2229357	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760254	0.82[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4760278	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs4760355	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs540730	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs56152729	0.87[EUR][1000 genomes]
rs61352607	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73119306	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7964492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7971133	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7974833	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Urate levels	23263486	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3741414	HOXC6	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57825600-57848600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:57841800-57846200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:57842000-57846000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:57843400-57844800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:57843600-57844600	Enhancers	HepG2	liver
6	chr12:57843600-57850400	Enhancers	Fetal Intestine Large	intestine
7	chr12:57844000-57844800	Enhancers	Liver	Liver
8	chr12:57844000-57850400	Enhancers	Fetal Intestine Small	intestine

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