Variant report

Variant	rs1553883
Chromosome Location	chr15:83472349-83472350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83417362..83419441-chr15:83470714..83472568,2	K562	blood:
2	chr15:83417408..83420922-chr15:83469506..83474317,6	K562	blood:
3	chr15:83464143..83466084-chr15:83470517..83472909,2	K562	blood:
4	chr15:83471021..83472960-chr15:83473027..83474704,2	K562	blood:
5	chr15:83418000..83420485-chr15:83471645..83474179,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250988	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1105867	1.00[CEU][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12385964	0.89[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap]
rs1256429	0.89[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs1256434	0.86[JPT][hapmap]
rs1256451	0.89[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes]
rs1256452	0.88[CEU][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap]
rs1256453	0.86[JPT][hapmap]
rs1256455	0.84[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap]
rs1256456	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12905235	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12910279	0.86[EUR][1000 genomes]
rs12914161	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17360083	0.86[JPT][hapmap]
rs1877241	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2089844	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2379992	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2379993	0.85[EUR][1000 genomes]
rs2458017	0.84[EUR][1000 genomes]
rs2621227	0.86[JPT][hapmap]
rs2621228	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs2667385	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs2890313	0.84[CEU][hapmap]
rs2928572	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs4238539	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4779063	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4779065	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7163402	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7169401	0.86[JPT][hapmap]
rs8038679	0.89[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap]
rs9806543	0.83[CHD][hapmap];0.86[JPT][hapmap]

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	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv977072	chr15:83467994-83473044	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1553883	RASGRF1	cis	cerebellum	SCAN
rs1553883	LOC402057	trans	multi-tissue	Pritchard
rs1553883	BTBD1	cis	parietal	SCAN
rs1553883	EFTUD1	cis	cerebellum	SCAN
rs1553883	BTBD1	cis	cerebellum	SCAN
rs1553883	RASGRF1	cis	parietal	SCAN
rs1553883	WHAMM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83450400-83477600	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:83469200-83477600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:83469400-83477600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:83469800-83477400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:83470000-83472600	Enhancers	Psoas Muscle	Psoas
6	chr15:83470200-83472600	Enhancers	Right Ventricle	heart
7	chr15:83471000-83477600	Weak transcription	Spleen	Spleen
8	chr15:83471200-83472600	Flanking Active TSS	Fetal Heart	heart
9	chr15:83471200-83478200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:83471800-83472800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr15:83471800-83473000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr15:83471800-83474000	Enhancers	K562	blood
13	chr15:83471800-83475000	Active TSS	Left Ventricle	heart
14	chr15:83472000-83472400	Enhancers	Fetal Muscle Trunk	muscle
15	chr15:83472000-83473400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:83472000-83475000	Active TSS	Right Atrium	heart
17	chr15:83472000-83477800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:83472200-83472400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:83472200-83472600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:83472200-83472600	Enhancers	Fetal Muscle Leg	muscle
21	chr15:83472200-83473400	Weak transcription	GM12878-XiMat	blood
22	chr15:83472200-83473600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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