Variant report

Variant	rs734408
Chromosome Location	chr6:39247346-39247347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39236174..39238959-chr6:39247299..39249650,2	MCF-7	breast:
2	chr6:39246289..39249933-chr6:39249942..39252765,4	MCF-7	breast:
3	chr6:39135484..39137595-chr6:39246692..39248573,2	MCF-7	breast:
4	chr6:39243650..39250520-chr6:39262135..39271800,15	MCF-7	breast:
5	chr6:39246522..39249278-chr6:39249658..39251560,2	MCF-7	breast:
6	chr6:39242418..39244408-chr6:39246030..39248375,3	MCF-7	breast:
7	chr6:39245951..39248389-chr6:39255673..39257874,2	MCF-7	breast:
8	chr6:39245598..39248423-chr6:39251437..39253909,2	K562	blood:
9	chr6:39195286..39197963-chr6:39246502..39249488,3	K562	blood:
10	chr6:39191982..39197381-chr6:39245126..39249052,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1005951	0.82[ASN][1000 genomes]
rs1005952	0.82[ASN][1000 genomes]
rs10947801	0.94[ASN][1000 genomes]
rs10947802	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11753890	0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11961984	0.84[ASN][1000 genomes]
rs12194671	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12195376	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12202277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12202455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12207643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12209091	0.94[ASN][1000 genomes]
rs12210847	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12211098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12214600	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13194563	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13214473	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1535497	0.87[ASN][1000 genomes]
rs1885616	0.94[ASN][1000 genomes]
rs1885617	0.94[ASN][1000 genomes]
rs1885618	0.94[ASN][1000 genomes]
rs1885621	0.94[ASN][1000 genomes]
rs2208791	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2758861	0.83[ASN][1000 genomes]
rs2758882	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2758883	0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2758884	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2758885	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2758887	0.94[ASN][1000 genomes]
rs2758888	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2758889	0.94[ASN][1000 genomes]
rs2758890	0.94[ASN][1000 genomes]
rs2758891	0.94[ASN][1000 genomes]
rs2758893	0.94[ASN][1000 genomes]
rs2758894	0.94[ASN][1000 genomes]
rs2758895	0.90[ASN][1000 genomes]
rs2758897	0.94[ASN][1000 genomes]
rs2758898	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2758899	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2758900	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2815016	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2815048	0.94[ASN][1000 genomes]
rs2815049	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2815050	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2815051	0.94[ASN][1000 genomes]
rs2815052	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2815053	0.87[ASN][1000 genomes]
rs2815054	0.94[ASN][1000 genomes]
rs2815057	0.94[ASN][1000 genomes]
rs36044810	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714234	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4714235	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59582961	0.92[ASN][1000 genomes]
rs62397165	0.82[ASN][1000 genomes]
rs62397166	0.87[ASN][1000 genomes]
rs62397167	0.94[ASN][1000 genomes]
rs62397168	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71556989	0.92[ASN][1000 genomes]
rs9369113	1.00[YRI][hapmap]
rs9380850	1.00[YRI][hapmap]
rs9394588	1.00[YRI][hapmap]
rs9462515	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9471040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9471043	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9471045	0.92[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:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39240400-39250200	Enhancers	Stomach Mucosa	stomach
2	chr6:39242000-39247400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:39242000-39247800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:39242600-39249600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:39243600-39247400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:39244400-39247600	Weak transcription	Pancreas	Pancrea
7	chr6:39245800-39248600	Enhancers	Placenta	Placenta
8	chr6:39246200-39251000	Enhancers	Liver	Liver
9	chr6:39246800-39248600	Enhancers	Small Intestine	intestine
10	chr6:39246800-39250400	Enhancers	Esophagus	oesophagus
11	chr6:39247000-39249000	Enhancers	Duodenum Mucosa	Duodenum
12	chr6:39247000-39250200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:39247000-39250200	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr6:39247000-39250400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr6:39247200-39247400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr6:39247200-39248600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:39247200-39249000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr6:39247200-39250400	Enhancers	Colonic Mucosa	Colon

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