Variant report

Variant	rs12408296
Chromosome Location	chr1:161684319-161684320
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000132185	Chromatin interaction
ENSG00000241347	Chromatin interaction
ENSG00000081721	Chromatin interaction
ENSG00000162746	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10753610	0.88[YRI][hapmap]
rs10917750	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs1340976	0.88[YRI][hapmap]
rs1340977	0.86[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1340978	0.86[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1340979	0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs1340980	0.87[ASN][1000 genomes]
rs1417582	0.93[CHB][hapmap]
rs1503813	0.80[CHB][hapmap]
rs1538971	0.86[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1891020	0.93[CHB][hapmap]
rs1954173	0.85[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs4657093	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57678166	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668534	0.88[YRI][hapmap]
rs74127102	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs905589	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv1822760	chr1:161480943-161687379	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12408296	FCRLA	Cis_1M	lymphoblastoid	RTeQTL
rs12408296	FREB	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161676200-161692000	Weak transcription	Spleen	Spleen
2	chr1:161682600-161689600	Weak transcription	K562	blood
3	chr1:161683600-161684600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:161683800-161684400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:161683800-161686000	Weak transcription	GM12878-XiMat	blood
6	chr1:161683800-161686800	Weak transcription	Primary B cells from cord blood	blood
7	chr1:161684200-161686600	Weak transcription	Primary B cells from peripheral blood	blood

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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

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