Variant report

Variant	rs7505834
Chromosome Location	chr18:12302598-12302599
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12287873..12290167-chr18:12301224..12302973,2	MCF-7	breast:
2	chr18:12270534..12272784-chr18:12301768..12304074,2	K562	blood:
3	chr18:12300999..12303281-chr18:12308137..12310057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267069	Chromatin interaction
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10459999	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10460000	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10460001	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10853225	0.81[EUR][1000 genomes]
rs11080564	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11080565	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11080569	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11080571	0.95[CEU][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap]
rs11080572	0.95[CEU][hapmap];0.89[JPT][hapmap]
rs1129115	0.95[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11553521	0.81[EUR][1000 genomes]
rs11662523	0.95[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs11665134	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12455770	0.83[EUR][1000 genomes]
rs12456857	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12968089	0.81[EUR][1000 genomes]
rs1941222	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs2298542	0.80[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap]
rs2298543	0.80[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap]
rs34314823	0.81[EUR][1000 genomes]
rs34829762	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35338639	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3786260	0.80[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap]
rs478088	0.80[CEU][hapmap]
rs4796961	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4796964	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4797677	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs4797680	0.80[CEU][hapmap];0.80[JPT][hapmap]
rs62098961	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7231182	0.95[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs7235296	0.95[CEU][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs7407640	0.95[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs7504908	0.95[CEU][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7504974	0.95[CEU][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8086821	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8086993	0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8087840	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8092506	1.00[CEU][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8097342	0.95[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs9303768	0.84[LWK][hapmap];0.82[MKK][hapmap]
rs9303769	0.95[CEU][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs9303770	0.80[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap]
rs9946698	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9951945	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9956171	0.80[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats 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	67 gene(s)	inside rSNPs	diseases
4	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7505834	MEST	trans	lymphoblastoid	seeQTL
rs7505834	TUBB6	cis	Whole Blood	GTEx
rs7505834	TUBB6	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12289000-12304800	Weak transcription	Pancreas	Pancrea
2	chr18:12289200-12306400	Weak transcription	Right Atrium	heart
3	chr18:12289400-12306400	Weak transcription	NHLF	lung
4	chr18:12294400-12306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:12301000-12303000	Enhancers	Fetal Heart	heart
6	chr18:12301600-12302600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr18:12301600-12303200	Enhancers	Placenta	Placenta
8	chr18:12301600-12305200	Weak transcription	Esophagus	oesophagus
9	chr18:12301800-12306200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr18:12302000-12303200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr18:12302000-12303200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr18:12302200-12302600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr18:12302200-12303200	Bivalent Enhancer	HepG2	liver
14	chr18:12302400-12303000	Flanking Active TSS	K562	blood
15	chr18:12302400-12303200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr18:12302400-12303200	Enhancers	NHEK	skin

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