Variant report

Variant	rs1792282
Chromosome Location	chr11:71135166-71135167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:71135115-71135425	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:71124009..71126373-chr11:71135133..71137138,2	K562	blood:
2	chr11:71122603..71125509-chr11:71135103..71137138,2	K562	blood:
3	chr11:71130483..71134539-chr11:71135016..71139274,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172900	TF binding region
ENSG00000172900	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10898144	0.92[EUR][1000 genomes]
rs11603330	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs11606033	0.81[CEU][hapmap]
rs12224205	0.83[ASN][1000 genomes]
rs12419279	1.00[CEU][hapmap]
rs12419334	0.84[TSI][hapmap]
rs12422045	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs12797951	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs1540127	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs1619577	0.85[ASN][1000 genomes]
rs1629220	0.85[ASN][1000 genomes]
rs1630498	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1790324	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1790328	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790330	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790339	0.85[ASN][1000 genomes]
rs1790340	0.83[ASN][1000 genomes]
rs1790341	0.85[ASN][1000 genomes]
rs1790343	0.85[ASN][1000 genomes]
rs1790344	0.85[ASN][1000 genomes]
rs1790345	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790350	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790353	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792224	0.85[ASN][1000 genomes]
rs1792226	0.85[ASN][1000 genomes]
rs1792227	0.85[ASN][1000 genomes]
rs1792229	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.85[ASN][1000 genomes]
rs1792231	0.85[ASN][1000 genomes]
rs1792233	0.85[ASN][1000 genomes]
rs1792234	0.94[CEU][hapmap];0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs1792235	0.85[ASN][1000 genomes]
rs1792264	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1792277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792280	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792281	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1792283	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792284	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1792315	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1894100	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2002064	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2017686	0.85[ASN][1000 genomes]
rs2276358	0.85[ASN][1000 genomes]
rs2276362	0.80[CEU][hapmap]
rs2282621	0.82[TSI][hapmap]
rs2511010	0.85[ASN][1000 genomes]
rs3750997	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs3794057	0.85[ASN][1000 genomes]
rs4402322	0.85[ASN][1000 genomes]
rs4435028	0.85[ASN][1000 genomes]
rs4616066	0.85[ASN][1000 genomes]
rs4944957	0.82[TSI][hapmap]
rs736894	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7928249	0.82[TSI][hapmap]
rs7935125	0.82[CEU][hapmap]

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	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1792282	AIP	cis	parietal	SCAN
rs1792282	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1792282	NADSYN1	cis	Nerve Tibial	GTEx
rs1792282	RP11-660L16.2	cis	Thyroid	GTEx
rs1792282	RAB6A	cis	cerebellum	SCAN
rs1792282	NADSYN1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71123600-71139600	Weak transcription	Right Atrium	heart
2	chr11:71132600-71144000	Weak transcription	Spleen	Spleen
3	chr11:71133800-71135400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:71133800-71135400	Enhancers	Primary B cells from peripheral blood	blood
5	chr11:71134000-71135200	Enhancers	Primary B cells from cord blood	blood
6	chr11:71134000-71135400	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr11:71134000-71135400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr11:71134000-71135400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:71134000-71135400	Enhancers	HMEC	breast
10	chr11:71134600-71135200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:71134600-71135400	Enhancers	Brain Substantia Nigra	brain
12	chr11:71134600-71135600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:71134800-71135400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:71135000-71135400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:71135000-71135400	Enhancers	GM12878-XiMat	blood
16	chr11:71135000-71136400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:71135000-71150600	Weak transcription	NH-A	brain

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