Variant report

Variant	rs11176082
Chromosome Location	chr12:66580735-66580736
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	chr12:66561525..66563608-chr12:66580703..66583177,2	K562	blood:
2	chr12:66578489..66581069-chr12:66583580..66586870,3	K562	blood:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10400539	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10735933	0.82[JPT][hapmap]
rs10878381	0.81[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10878382	0.81[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10878383	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10878389	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10878391	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176043	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11176054	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11176056	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11176063	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11176065	0.84[ASN][1000 genomes]
rs11176067	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176068	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176078	0.92[CEU][hapmap];0.97[CHD][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11176080	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176081	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12832926	0.81[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17767200	0.81[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1882201	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1898304	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1921083	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2141709	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2178486	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2870781	0.81[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34645929	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34755483	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4474482	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4575321	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56271210	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61927092	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7295147	0.81[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7302893	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7305938	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7966453	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7966561	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7979029	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7979775	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv541516	chr12:66547969-66596036	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv899215	chr12:66556960-66594134	Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	n/a
6	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv541517	chr12:66576953-66639823	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11176082	LLPH	cis	cerebellum	SCAN
rs11176082	TMBIM4	cis	uninvolved skin	skin_eQTL
rs11176082	RP11-745O10.2	cis	Artery Tibial	GTEx
rs11176082	TMBIM4	cis	cerebellum	SCAN
rs11176082	TMBIM4	cis	lymphoblastoid	seeQTL
rs11176082	TMBIM4	cis	parietal	SCAN
rs11176082	FLJ23235	trans	multi-tissue	Pritchard
rs11176082	RP11-745O10.2	cis	Whole Blood	GTEx
rs11176082	TMBIM4	cis	normal skin	skin_eQTL
rs11176082	TMBIM4	cis	lesional skin	skin_eQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66579600-66582400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:66580400-66581600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr12:66580600-66580800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:66580600-66582400	Enhancers	Primary B cells from cord blood	blood
5	chr12:66580600-66583000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links