Variant report

Variant	rs1183892
Chromosome Location	chr12:66571266-66571267
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66560846..66563703-chr12:66570897..66572814,2	K562	blood:
2	chr12:66570661..66572865-chr12:66583805..66585652,2	K562	blood:
3	chr12:66570441..66572805-chr12:66575198..66577758,3	K562	blood:
4	chr12:66570441..66574435-chr12:66574821..66579186,5	K562	blood:
5	chr12:66562178..66565316-chr12:66569101..66574055,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10878378	0.91[EUR][1000 genomes]
rs11176060	0.89[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1168735	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168745	0.92[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1168765	0.89[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs1168766	0.92[EUR][1000 genomes]
rs1168770	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs1177578	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs1184556	0.92[EUR][1000 genomes]
rs1184884	0.92[EUR][1000 genomes]
rs1185888	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823890	0.84[EUR][1000 genomes]
rs1370126	0.91[EUR][1000 genomes]
rs1436849	0.92[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576187	0.90[EUR][1000 genomes]
rs2870782	0.88[EUR][1000 genomes]
rs4296075	0.83[EUR][1000 genomes]
rs4328252	0.92[EUR][1000 genomes]
rs7975029	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs7979576	0.88[EUR][1000 genomes]
rs8793	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1183892	TMBIM4	cis	cerebellum	SCAN
rs1183892	TMBIM4	cis	normal skin	skin_eQTL
rs1183892	TMBIM4	cis	lesional skin	skin_eQTL
rs1183892	RP11-745O10.2	cis	Esophagus Mucosa	GTEx
rs1183892	TMBIM4	cis	uninvolved skin	skin_eQTL
rs1183892	RP11-745O10.2	cis	Heart Left Ventricle	GTEx
rs1183892	RP11-745O10.2	cis	Artery Tibial	GTEx
rs1183892	TMBIM4	cis	parietal	SCAN
rs1183892	RP11-745O10.2	cis	Stomach	GTEx
rs1183892	RP11-745O10.2	cis	lung	GTEx
rs1183892	RP11-745O10.2	cis	Thyroid	GTEx
rs1183892	RP11-745O10.2	cis	Whole Blood	GTEx
rs1183892	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs1183892	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66569000-66571600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr12:66569800-66571400	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr12:66570000-66571400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:66570400-66572000	Enhancers	Fetal Lung	lung
5	chr12:66571200-66571400	Bivalent Enhancer	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links