Variant report

Variant	rs12420069
Chromosome Location	chr11:65010957-65010958
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11605576	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12420456	0.92[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs17583	0.90[JPT][hapmap]
rs2271448	0.80[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2277307	0.90[JPT][hapmap]
rs3782093	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs3825072	0.90[JPT][hapmap]
rs3953797	0.90[JPT][hapmap]
rs56657874	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv976461	chr11:65000821-65054446	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12420069	CLCF1	cis	parietal	SCAN
rs12420069	SCGB1A1	cis	parietal	SCAN
rs12420069	SLC22A24	cis	cerebellum	SCAN
rs12420069	SLC22A20	cis	Skin Sun Exposed Lower leg	GTEx
rs12420069	PCNXL3	cis	parietal	SCAN
rs12420069	HRASLS2	cis	parietal	SCAN
rs12420069	DAGLA	cis	parietal	SCAN
rs12420069	RBM14	cis	parietal	SCAN
rs12420069	NUDT8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64993600-65011000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:65004600-65011200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:65009800-65016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:65010600-65011200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:65010600-65011200	Weak transcription	Fetal Intestine Small	intestine
6	chr11:65010600-65011800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr11:65010800-65011000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr11:65010800-65011200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr11:65010800-65011400	Enhancers	H9 Cell Line	embryonic stem cell
10	chr11:65010800-65011800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr11:65010800-65011800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr11:65010800-65012000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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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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