Variant report

Variant	rs17079029
Chromosome Location	chr6:150239330-150239331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150237859..150240008-chr6:150242454..150244236,2	K562	blood:
2	chr6:150238077..150241849-chr6:150242731..150245993,5	MCF-7	breast:
3	chr6:150226570..150229723-chr6:150237444..150240125,3	K562	blood:
4	chr6:150186409..150189034-chr6:150239066..150241266,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203722	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10457853	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2342773	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4142628	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6557137	1.00[CEU][hapmap];0.84[CHD][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6557163	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6904335	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6905778	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6910351	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6915465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6927913	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6936944	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72997594	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7745070	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7761734	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9322226	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9322227	1.00[CEU][hapmap];0.84[CHD][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9322230	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9322231	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9371216	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9371523	0.90[EUR][1000 genomes]
rs9371539	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9371555	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9383569	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9383573	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9383583	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9383916	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9383942	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9383943	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9383944	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383945	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9397049	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9397053	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9397056	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9397057	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9397060	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9397071	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9397394	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9397399	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9397419	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9397447	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9397449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9397451	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv970172	chr6:150235248-150244455	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17079029	LRP11	cis	parietal	SCAN
rs17079029	LRP11	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150226200-150242000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:150227800-150243400	Weak transcription	Right Ventricle	heart
3	chr6:150230400-150243600	Weak transcription	Pancreas	Pancrea
4	chr6:150237200-150243600	Weak transcription	Right Atrium	heart
5	chr6:150238400-150239800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:150238800-150239400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:150238800-150239600	Enhancers	NHEK	skin
8	chr6:150239000-150239400	Enhancers	HMEC	breast
9	chr6:150239000-150239600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:150239000-150239800	Enhancers	Esophagus	oesophagus
11	chr6:150239200-150239400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:150239200-150239600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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