Variant report

Variant	rs2046070
Chromosome Location	chr15:83641784-83641785
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83641083..83642677-chr15:83653186..83655215,2	MCF-7	breast:
2	chr15:83620099..83621700-chr15:83641187..83642969,2	MCF-7	breast:
3	chr15:83638292..83642074-chr15:83644937..83647972,4	K562	blood:
4	chr15:83639890..83641913-chr15:83646413..83649279,2	MCF-7	breast:
5	chr15:83639457..83641351-chr15:83641734..83644716,2	MCF-7	breast:
6	chr15:83631654..83637396-chr15:83638049..83642550,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103942	Chromatin interaction
ENSG00000169612	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1037403	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11259960	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs11259963	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050725	0.94[JPT][hapmap]
rs12148275	0.81[CHB][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap]
rs12441675	0.94[JPT][hapmap]
rs1568657	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2061947	0.94[JPT][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap]
rs2123157	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2123158	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2167602	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2381028	0.96[ASN][1000 genomes]
rs28451607	0.97[ASN][1000 genomes]
rs28510273	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4842859	0.91[ASN][1000 genomes]
rs4842928	0.92[ASN][1000 genomes]
rs4842935	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4843141	0.94[JPT][hapmap]
rs4843144	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs4843146	0.86[JPT][hapmap]
rs59108707	0.87[ASN][1000 genomes]
rs6603038	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603041	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8025253	0.98[ASN][1000 genomes]
rs8034220	0.84[ASN][1000 genomes]
rs8043020	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs872598	0.89[JPT][hapmap];0.83[TSI][hapmap]
rs872599	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2046070	WHAMM	cis	cerebellum	SCAN
rs2046070	TM6SF1	cis	cerebellum	SCAN
rs2046070	BTBD1	cis	parietal	SCAN
rs2046070	WHAMM	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83622200-83649400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:83635600-83653800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:83635800-83654000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:83637800-83642000	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr15:83639800-83641800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:83640000-83642400	Enhancers	Liver	Liver
7	chr15:83640200-83641800	Weak transcription	HSMM	muscle
8	chr15:83640200-83654000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:83640600-83641800	Weak transcription	Pancreas	Pancrea
10	chr15:83640600-83654000	Weak transcription	HSMMtube	muscle
11	chr15:83640800-83654000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:83641200-83653800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:83641200-83654200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:83641400-83642200	Enhancers	Rectal Mucosa Donor 29	rectum

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