Variant report

Variant	rs17276520
Chromosome Location	chr4:153039401-153039402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:153033738..153036508-chr4:153038629..153040300,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11721407	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11726930	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11727188	0.80[AMR][1000 genomes]
rs11727245	0.87[ASN][1000 genomes]
rs11727862	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11732677	0.83[MEX][hapmap]
rs11733393	0.85[AMR][1000 genomes]
rs11734900	0.87[ASN][1000 genomes]
rs11736628	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11737156	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13107968	0.87[ASN][1000 genomes]
rs13112841	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13131134	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13147317	0.83[ASN][1000 genomes]
rs13151283	0.90[ASN][1000 genomes]
rs17276450	0.90[ASN][1000 genomes]
rs17361216	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17361258	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1991223	0.87[MEX][hapmap]
rs2406622	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28531716	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34067446	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34069606	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34276148	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34509512	0.90[ASN][1000 genomes]
rs34771630	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34909306	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35296212	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35336515	0.90[ASN][1000 genomes]
rs35897176	0.90[ASN][1000 genomes]
rs66476112	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6843300	0.83[ASN][1000 genomes]
rs7662581	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7674458	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7675481	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7682931	0.88[AMR][1000 genomes];0.85[EUR][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	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv880774	chr4:153035743-153121818	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17276520	RP11-18H21.1	cis	Whole Blood	GTEx
rs17276520	DCLK2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:153023800-153040000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:153031600-153040000	Weak transcription	Right Ventricle	heart
3	chr4:153033200-153040800	Enhancers	Fetal Thymus	thymus
4	chr4:153034200-153040000	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr4:153035000-153040200	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr4:153035400-153040600	Enhancers	Thymus	Thymus
7	chr4:153036200-153040600	Enhancers	Fetal Muscle Leg	muscle
8	chr4:153036600-153040600	Enhancers	Dnd41	blood
9	chr4:153037600-153040000	Weak transcription	Lung	lung
10	chr4:153037600-153040200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr4:153037600-153040600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr4:153037800-153039600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr4:153038400-153039800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr4:153038600-153039600	Enhancers	Fetal Heart	heart
15	chr4:153038800-153039600	Enhancers	Fetal Brain Male	brain
16	chr4:153038800-153040600	Enhancers	Fetal Muscle Trunk	muscle
17	chr4:153038800-153040600	Enhancers	Psoas Muscle	Psoas
18	chr4:153038800-153040800	Enhancers	Fetal Stomach	stomach
19	chr4:153038800-153041600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr4:153038800-153043200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:153039200-153040600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:153039400-153040400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:153039400-153040400	Weak transcription	Left Ventricle	heart

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