Variant report

Variant	rs2758883
Chromosome Location	chr6:39249653-39249654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39246289..39249933-chr6:39249942..39252765,4	MCF-7	breast:
2	chr6:39243650..39250520-chr6:39262135..39271800,15	MCF-7	breast:
3	chr6:39195713..39197963-chr6:39247882..39249799,3	K562	blood:
4	chr6:39249494..39252314-chr6:39258691..39261153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1005951	0.82[ASN][1000 genomes]
rs1005952	0.82[ASN][1000 genomes]
rs10947801	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947802	0.94[ASN][1000 genomes]
rs11753890	0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs11961984	0.85[ASN][1000 genomes]
rs12194671	0.82[ASN][1000 genomes]
rs12195376	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12202277	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12202455	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12207643	0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12209091	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210847	0.94[ASN][1000 genomes]
rs12211098	0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12214600	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13194563	0.84[ASN][1000 genomes]
rs13214473	0.97[ASN][1000 genomes]
rs1535497	0.88[ASN][1000 genomes]
rs1885616	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885617	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885618	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885621	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758882	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758884	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758885	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758887	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758888	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758889	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758890	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758891	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758893	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758894	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758895	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2758897	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758898	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758899	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758900	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2758907	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2815016	0.82[ASN][1000 genomes]
rs2815048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815049	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815050	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815051	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815052	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815053	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2815054	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815057	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36044810	0.88[ASN][1000 genomes]
rs4711593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4714234	0.81[ASN][1000 genomes]
rs4714235	0.91[ASN][1000 genomes]
rs59582961	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62397165	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62397166	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62397167	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62397168	0.97[ASN][1000 genomes]
rs71556989	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs734408	0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9462515	0.97[ASN][1000 genomes]
rs9471040	0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9471043	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9471045	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39240400-39250200	Enhancers	Stomach Mucosa	stomach
2	chr6:39246200-39251000	Enhancers	Liver	Liver
3	chr6:39246800-39250400	Enhancers	Esophagus	oesophagus
4	chr6:39247000-39250200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:39247000-39250200	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr6:39247000-39250400	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr6:39247200-39250400	Enhancers	Colonic Mucosa	Colon
8	chr6:39248200-39250200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:39248400-39263400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:39248400-39263400	Weak transcription	Right Atrium	heart
11	chr6:39248800-39252800	Weak transcription	Spleen	Spleen
12	chr6:39249000-39249800	Enhancers	Small Intestine	intestine
13	chr6:39249000-39250600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:39249200-39249800	Bivalent Enhancer	Fetal Intestine Large	intestine
15	chr6:39249200-39250000	Bivalent Enhancer	Fetal Intestine Small	intestine
16	chr6:39249400-39249800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr6:39249400-39250800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:39249600-39249800	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr6:39249600-39250600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:39249600-39253200	Weak transcription	Gastric	stomach

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