Variant report

Variant	rs2379994
Chromosome Location	chr15:83472507-83472508
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: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11259951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11635618	0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11856316	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11856878	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12903359	0.86[ASN][1000 genomes]
rs12905388	0.87[CHB][hapmap]
rs12910606	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17158263	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1828510	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2046071	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs34541883	0.85[ASN][1000 genomes]
rs35788008	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4778691	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7174089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7182990	0.85[ASN][1000 genomes]
rs8042254	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2379994	WHAMM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:23 , 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	chr15:83472000-83473400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:83472000-83475000	Active TSS	Right Atrium	heart
16	chr15:83472000-83477800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:83472200-83472600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:83472200-83472600	Enhancers	Fetal Muscle Leg	muscle
19	chr15:83472200-83473400	Weak transcription	GM12878-XiMat	blood
20	chr15:83472200-83473600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:83472400-83472600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr15:83472400-83473200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:83472400-83478200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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