Variant report

Variant	rs11634042
Chromosome Location	chr15:79105350-79105351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:79105202..79107134-chrX:78755858..78757584,2	MCF-7	breast:
2	chr15:79105247..79107755-chr15:79157087..79159923,2	MCF-7	breast:
3	chr15:79102834..79106085-chr15:79164025..79165931,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185787	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11072803	0.81[AMR][1000 genomes]
rs11072804	0.84[AMR][1000 genomes]
rs11072806	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11631955	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11632102	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11634450	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11638321	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11639044	0.92[CEU][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11856536	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11858210	0.83[AMR][1000 genomes]
rs12050525	0.80[AMR][1000 genomes]
rs12592721	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592762	0.85[JPT][hapmap]
rs12899147	0.96[CEU][hapmap];0.88[CHB][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12903203	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1809420	0.84[MEX][hapmap]
rs1825087	0.84[AMR][1000 genomes]
rs1994016	0.85[CEU][hapmap];0.88[CHB][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs2277545	0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2277546	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28610385	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2904220	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3825807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886592	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4887113	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7173267	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7177699	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	122 gene(s)	inside rSNPs	diseases
2	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904432	chr15:79066932-79175813	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv3334366	chr15:79102897-79105495	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11634042	CLK3	cis	parietal	SCAN
rs11634042	CPLX3	cis	cerebellum	SCAN
rs11634042	CHRNA5	cis	parietal	SCAN
rs11634042	BCL2A1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79103800-79105400	Enhancers	Spleen	Spleen
2	chr15:79104200-79106000	Weak transcription	Fetal Kidney	kidney
3	chr15:79104600-79105400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr15:79104800-79105400	Enhancers	Brain Cingulate Gyrus	brain
5	chr15:79104800-79105400	Enhancers	Gastric	stomach
6	chr15:79104800-79106000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:79104800-79106800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:79104800-79117800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:79104800-79117800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr15:79105000-79106800	Weak transcription	Fetal Brain Female	brain
11	chr15:79105000-79108400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:79105000-79110800	Weak transcription	Right Atrium	heart
13	chr15:79105000-79117800	Weak transcription	HSMMtube	muscle
14	chr15:79105000-79118000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:79105200-79106200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:79105200-79110200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:79105200-79118000	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links