Variant report

Variant	rs10456082
Chromosome Location	chr6:35991474-35991475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:35989631..35991616-chr6:35995503..35997016,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112062	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10456438	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190116	0.94[EUR][1000 genomes]
rs12204910	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12206103	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16883819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16883860	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16883989	0.92[ASN][1000 genomes]
rs16884628	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16884660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16884694	0.86[CHB][hapmap]
rs16884906	0.92[ASN][1000 genomes]
rs16884919	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2237094	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2237096	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3730327	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3730366	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3761980	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs3804451	1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs41271263	0.87[ASN][1000 genomes]
rs55878630	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56059109	0.92[ASN][1000 genomes]
rs56133220	0.92[ASN][1000 genomes]
rs56156688	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs56327416	0.92[ASN][1000 genomes]
rs56362075	0.92[ASN][1000 genomes]
rs56413204	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs56715462	0.92[ASN][1000 genomes]
rs58390233	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs58583792	0.92[ASN][1000 genomes]
rs58690654	0.92[ASN][1000 genomes]
rs60100837	0.92[ASN][1000 genomes]
rs60342497	0.92[ASN][1000 genomes]
rs60481532	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs60909394	0.92[ASN][1000 genomes]
rs61195139	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs61212706	0.92[ASN][1000 genomes]
rs61364424	0.92[ASN][1000 genomes]
rs61763101	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6457878	1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs6906520	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6908622	0.92[ASN][1000 genomes]
rs6910685	0.92[ASN][1000 genomes]
rs6914570	0.92[ASN][1000 genomes]
rs6921999	0.87[ASN][1000 genomes]
rs6930333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6932598	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6934216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs73407868	0.92[ASN][1000 genomes]
rs73407870	0.92[ASN][1000 genomes]
rs73407871	0.92[ASN][1000 genomes]
rs73407876	0.92[ASN][1000 genomes]
rs73409842	0.89[ASN][1000 genomes]
rs73729685	0.88[ASN][1000 genomes]
rs73729698	0.92[ASN][1000 genomes]
rs73730437	0.92[ASN][1000 genomes]
rs73730440	0.92[ASN][1000 genomes]
rs7745082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7745536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7745927	0.92[ASN][1000 genomes]
rs7747846	0.89[ASN][1000 genomes]
rs7748078	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7759175	0.92[ASN][1000 genomes]
rs7760405	0.86[CHB][hapmap]
rs7760578	0.92[ASN][1000 genomes]
rs7761118	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7764494	0.86[CHB][hapmap]
rs7766032	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7770183	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.80[ASN][1000 genomes]
rs7771484	0.86[CHB][hapmap]
rs7772088	0.92[ASN][1000 genomes]
rs7775290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription 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 target site	41 gene(s)	inside rSNPs	diseases
2	nsv528432	chr6:35958871-36035354	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10456082	SLC26A8	cis	parietal	SCAN
rs10456082	SLC26A8	cis	cerebellum	SCAN
rs10456082	MAPK13	cis	cerebellum	SCAN
rs10456082	SLC26A8	cis	Thyroid	GTEx
rs10456082	ZFAND3	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35964800-35991800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:35987200-35991600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:35987400-35991600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:35987400-35991600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:35988200-35991600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr6:35988400-35991600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:35990000-35991600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr6:35991400-35991600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:35991400-35991600	Enhancers	Primary hematopoietic stem cells	blood
10	chr6:35991400-35991800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:35991400-35991800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr6:35991400-35991800	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr6:35991400-35992000	Active TSS	Primary B cells from cord blood	blood

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