Variant report

Variant	rs12700742
Chromosome Location	chr7:26562943-26562944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:26561471..26564248-chr7:26575728..26578008,2	MCF-7	breast:
2	chr7:26554794..26556957-chr7:26561161..26563365,2	MCF-7	breast:
3	chr7:26403874..26406286-chr7:26561815..26564563,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf71-6	chr7:26560953-26563344	NONHSAT119645

Variant related genes	Relation type
ENSG00000086300	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1047022	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1076284	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs12537002	0.92[ASN][1000 genomes]
rs12700741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700746	0.86[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs13243495	0.81[ASN][1000 genomes]
rs17153874	0.81[ASN][1000 genomes]
rs17283843	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs2190186	0.86[JPT][hapmap]
rs2391282	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2391284	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs34066752	0.81[ASN][1000 genomes]
rs35496114	0.81[ASN][1000 genomes]
rs3757656	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs4289709	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs4719871	0.92[ASN][1000 genomes]
rs4719872	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722605	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4722606	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4722607	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722609	0.81[ASN][1000 genomes]
rs6943220	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6957136	0.92[ASN][1000 genomes]
rs6957786	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs6968080	0.92[ASN][1000 genomes]
rs6968655	0.83[ASN][1000 genomes]
rs71521773	0.81[ASN][1000 genomes]
rs71521774	0.81[ASN][1000 genomes]
rs71521775	0.81[ASN][1000 genomes]
rs71521777	0.81[ASN][1000 genomes]
rs73063761	0.92[ASN][1000 genomes]
rs73063763	0.86[ASN][1000 genomes]
rs73063794	0.92[ASN][1000 genomes]
rs740185	0.81[ASN][1000 genomes]
rs740186	0.81[ASN][1000 genomes]
rs740187	0.81[ASN][1000 genomes]
rs757804	0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs886716	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs886717	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs886719	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12700742	NFE2L3	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links