Variant report

Variant	rs6772917
Chromosome Location	chr3:142938456-142938457
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	chr3:142935120..142937637-chr3:142937877..142939570,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11708440	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715203	0.85[ASN][1000 genomes]
rs1550548	0.84[ASN][1000 genomes]
rs1667712	0.82[ASN][1000 genomes]
rs169808	0.86[ASN][1000 genomes]
rs17470719	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs186077	0.85[ASN][1000 genomes]
rs2165519	0.87[ASN][1000 genomes]
rs2165520	0.85[ASN][1000 genomes]
rs2165521	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583458	0.84[ASN][1000 genomes]
rs2596616	0.83[ASN][1000 genomes]
rs294465	0.85[ASN][1000 genomes]
rs294469	0.86[ASN][1000 genomes]
rs294471	0.85[ASN][1000 genomes]
rs294472	0.86[ASN][1000 genomes]
rs294473	0.86[ASN][1000 genomes]
rs4371486	0.82[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs4683461	0.89[CHB][hapmap]
rs4839588	0.85[ASN][1000 genomes]
rs4839591	0.85[ASN][1000 genomes]
rs4839616	0.86[ASN][1000 genomes]
rs4839617	0.86[ASN][1000 genomes]
rs4839618	0.86[ASN][1000 genomes]
rs4839619	0.85[ASN][1000 genomes]
rs4839621	0.86[ASN][1000 genomes]
rs4839629	0.85[ASN][1000 genomes]
rs4839637	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839656	0.85[ASN][1000 genomes]
rs54520	0.84[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs57923975	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62279674	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6414352	0.86[ASN][1000 genomes]
rs6440149	0.86[ASN][1000 genomes]
rs6440150	0.86[ASN][1000 genomes]
rs6440151	0.86[ASN][1000 genomes]
rs6440152	0.86[ASN][1000 genomes]
rs6440153	0.85[ASN][1000 genomes]
rs6440154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765181	0.85[ASN][1000 genomes]
rs67665960	0.84[EUR][1000 genomes]
rs6776634	0.85[ASN][1000 genomes]
rs6777882	0.85[ASN][1000 genomes]
rs6778330	0.85[ASN][1000 genomes]
rs6781821	0.84[ASN][1000 genomes]
rs6781909	0.86[ASN][1000 genomes]
rs6785002	0.85[ASN][1000 genomes]
rs6785085	0.83[ASN][1000 genomes]
rs6786129	0.86[ASN][1000 genomes]
rs6787156	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6795908	0.85[ASN][1000 genomes]
rs6796353	0.85[ASN][1000 genomes]
rs6803862	0.86[ASN][1000 genomes]
rs6808316	0.88[ASN][1000 genomes]
rs7611317	0.84[ASN][1000 genomes]
rs7622977	0.82[ASN][1000 genomes]
rs7632649	0.86[ASN][1000 genomes]
rs7642629	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7646566	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs834906	0.85[ASN][1000 genomes]
rs834907	0.86[ASN][1000 genomes]
rs834908	0.86[ASN][1000 genomes]
rs834909	0.86[ASN][1000 genomes]
rs834910	0.86[ASN][1000 genomes]
rs9289656	0.85[ASN][1000 genomes]
rs9289657	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs967846	1.00[YRI][hapmap]
rs9809153	0.84[ASN][1000 genomes]
rs9821086	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9830629	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831427	0.86[EUR][1000 genomes]
rs9847552	0.81[ASN][1000 genomes]
rs9874117	0.86[EUR][1000 genomes]
rs990738	0.85[ASN][1000 genomes]
rs991419	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv508250	chr3:142842454-142943722	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv34280	chr3:142887460-142962075	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv818171	chr3:142894411-142960273	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1009573	chr3:142896048-142959777	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv2757014	chr3:142905661-142964373	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142935000-142940600	Enhancers	Fetal Thymus	thymus
2	chr3:142936400-142940600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:142936400-142941400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr3:142936400-142942600	Weak transcription	Fetal Lung	lung
5	chr3:142936400-142945600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:142936600-142941200	Weak transcription	K562	blood
7	chr3:142937600-142938600	Weak transcription	Primary T cells from cord blood	blood
8	chr3:142937600-142940600	Enhancers	Dnd41	blood
9	chr3:142937600-142947600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:142937800-142938800	Weak transcription	Primary B cells from cord blood	blood
11	chr3:142937800-142939200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:142937800-142941400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:142938000-142939200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:142938000-142939200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:142938000-142939200	Weak transcription	Thymus	Thymus
16	chr3:142938000-142939400	Weak transcription	GM12878-XiMat	blood
17	chr3:142938000-142941400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links