Variant report

Variant	rs10943253
Chromosome Location	chr6:76212117-76212118
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:76209916..76212546-chr6:76311057..76312919,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112701	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10806043	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10943273	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs12196108	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12199441	0.83[ASN][1000 genomes]
rs12199457	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs12213227	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13214795	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs1336043	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1414597	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2647399	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs2647400	0.81[JPT][hapmap]
rs2647401	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs2647402	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs2647415	0.88[CEU][hapmap]
rs2647418	0.96[CEU][hapmap];0.85[YRI][hapmap]
rs2703662	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2783351	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs2784730	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs2808182	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2808186	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2808187	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2842535	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs2951917	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2951920	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2998367	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs35402776	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4708189	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs570939	0.89[CEU][hapmap]
rs575720	0.88[CEU][hapmap]
rs649935	0.88[CEU][hapmap]
rs6911868	0.88[CEU][hapmap]
rs6936251	0.88[CEU][hapmap]
rs7768713	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9294001	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs9343290	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9352237	0.88[CEU][hapmap]
rs9443180	0.84[ASN][1000 genomes]
rs9447490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9447493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9447503	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9447510	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs9447513	0.84[ASN][1000 genomes]
rs9447514	0.83[ASN][1000 genomes]
rs9447522	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap]
rs9885866	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS 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	70 gene(s)	inside rSNPs	diseases
3	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv1022428	chr6:76023118-76575620	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
5	nsv538312	chr6:76023118-76575620	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv1032245	chr6:76045537-76545703	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv538313	chr6:76045537-76545703	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
8	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
10	nsv603770	chr6:76200514-76277296	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv5353	chr6:76205962-76218316	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10943253	SENP6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76203200-76214400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:76203800-76214400	Weak transcription	Left Ventricle	heart
3	chr6:76203800-76215000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:76205000-76213600	Enhancers	HUVEC	blood vessel
5	chr6:76205400-76213200	Weak transcription	NHLF	lung
6	chr6:76208800-76212800	Weak transcription	Fetal Lung	lung
7	chr6:76209000-76214400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:76209000-76215000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:76209800-76212200	Enhancers	A549	lung
10	chr6:76209800-76212600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:76209800-76214400	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:76209800-76214400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:76211800-76212600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links