Variant report

Variant	rs12939306
Chromosome Location	chr17:38008508-38008509
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	chr17:38004767..38008555-chr17:38017604..38021491,3	K562	blood:

Variant related genes	Relation type
ENSG00000161405	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12943012	0.81[AFR][1000 genomes]
rs12943472	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12945253	0.86[YRI][hapmap]
rs12946188	0.86[YRI][hapmap]
rs12947480	0.92[YRI][hapmap]
rs12948686	0.82[AFR][1000 genomes]
rs12949178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12950066	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12953265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13313564	0.81[YRI][hapmap]
rs1377562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28420939	0.84[AFR][1000 genomes]
rs28651240	0.82[AFR][1000 genomes]
rs34020832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34225322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34455157	0.96[AFR][1000 genomes]
rs34523816	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34572227	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35789812	0.91[AFR][1000 genomes]
rs36049276	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs66565390	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs67135703	0.91[AFR][1000 genomes]
rs73304137	0.96[AFR][1000 genomes]
rs8073948	1.00[YRI][hapmap]
rs8079075	0.84[YRI][hapmap]
rs9900019	0.86[YRI][hapmap]
rs9900538	0.83[YRI][hapmap]
rs9907096	0.86[YRI][hapmap]
rs9907966	0.84[YRI][hapmap]
rs9911688	0.84[YRI][hapmap]
rs9913769	0.84[YRI][hapmap]
rs9913957	0.84[YRI][hapmap]
rs9915509	0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs9916259	0.84[YRI][hapmap]
rs9916369	0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs9941360	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv1795575	chr17:37974075-38041762	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv3356491	chr17:38005976-38008624	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38000800-38017400	Weak transcription	Thymus	Thymus
2	chr17:38004000-38010800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr17:38004400-38008600	Weak transcription	Pancreas	Pancrea
4	chr17:38004400-38016800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr17:38005200-38014200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr17:38006200-38008600	Weak transcription	Primary T cells from cord blood	blood
7	chr17:38006200-38008800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:38006200-38017400	Weak transcription	Fetal Thymus	thymus
9	chr17:38007200-38016600	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr17:38007400-38009400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr17:38007400-38009600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:38007400-38010600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr17:38007600-38008600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr17:38007800-38009200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr17:38007800-38009600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr17:38007800-38009800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr17:38007800-38010200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr17:38008200-38009600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr17:38008400-38009000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr17:38008400-38009400	Enhancers	K562	blood
21	chr17:38008400-38009600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr17:38008400-38009600	Flanking Active TSS	GM12878-XiMat	blood
23	chr17:38008400-38012800	Genic enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links