Variant report

Variant	rs4236504
Chromosome Location	chr7:86776112-86776113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:86774241..86777874-chr7:86780751..86783070,4	MCF-7	breast:
2	chr7:86758739..86761161-chr7:86775271..86777387,2	K562	blood:

Variant related genes	Relation type
ENSG00000135164	Chromatin interaction
ENSG00000224046	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1011952	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1011953	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10245036	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs10263920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10273826	0.94[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs1058972	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1558050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1574795	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2106955	0.99[EUR][1000 genomes]
rs2286267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810883	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4728685	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4728688	0.83[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs4728690	0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.82[YRI][hapmap]
rs6465099	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6465100	0.85[EUR][1000 genomes]
rs6942878	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6952842	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6957785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964225	0.96[YRI][hapmap]
rs6966613	0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[ASN][1000 genomes]
rs6975175	0.85[EUR][1000 genomes]
rs6978590	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs757159	1.00[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs769156	1.00[CEU][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs7776634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7792031	0.81[CEU][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs7793356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7800541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7812191	0.83[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	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1015870	chr7:86490491-86802320	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
5	nsv539000	chr7:86490491-86802320	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
6	nsv527889	chr7:86496042-86832603	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1028503	chr7:86684514-86778047	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1016761	chr7:86758544-86914152	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4236504	C7orf23	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86771000-86780800	Weak transcription	Fetal Intestine Large	intestine
2	chr7:86771400-86780400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:86774600-86780400	Weak transcription	GM12878-XiMat	blood
4	chr7:86774600-86780600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr7:86774600-86780800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:86775800-86776400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr7:86776000-86776600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr7:86776000-86776800	Enhancers	Fetal Muscle Trunk	muscle
9	chr7:86776000-86777000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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