Variant report

Variant	rs1388240
Chromosome Location	chr4:127657442-127657443
allele	G/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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:127655542..127661109-chr4:127874426..127880524,8	K562	blood:
2	chr4:127654180..127658212-chr4:127693803..127700290,9	K562	blood:
3	chr4:127656785..127658564-chr4:127670907..127672656,2	K562	blood:
4	chr4:127654180..127661020-chr4:127693803..127700410,12	K562	blood:
5	chr4:127656956..127659808-chr4:155413444..155414968,2	K562	blood:
6	chr4:127655557..127658334-chr4:127703330..127706969,3	K562	blood:
7	chr4:127656968..127658978-chr4:127715572..127717474,3	K562	blood:

No data

Extended variants
information (count: 129 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1032819	0.95[ASN][1000 genomes]
rs1032820	0.89[ASN][1000 genomes]
rs10518505	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518506	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518507	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857118	0.95[ASN][1000 genomes]
rs11098890	0.95[ASN][1000 genomes]
rs11098895	0.83[ASN][1000 genomes]
rs1167189	0.98[ASN][1000 genomes]
rs11722194	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11724202	0.91[ASN][1000 genomes]
rs11730606	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734063	0.83[ASN][1000 genomes]
rs12499781	0.95[ASN][1000 genomes]
rs12500556	0.95[ASN][1000 genomes]
rs12506431	0.95[ASN][1000 genomes]
rs12507245	0.87[ASN][1000 genomes]
rs12510029	0.95[ASN][1000 genomes]
rs12512290	0.95[ASN][1000 genomes]
rs12642024	0.91[ASN][1000 genomes]
rs12642095	0.81[ASN][1000 genomes]
rs12642632	0.83[ASN][1000 genomes]
rs12646727	0.84[ASN][1000 genomes]
rs12647245	0.82[ASN][1000 genomes]
rs12649784	1.00[JPT][hapmap]
rs13101665	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13104073	0.97[ASN][1000 genomes]
rs13105260	0.89[ASN][1000 genomes]
rs13105329	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13111812	1.00[ASN][1000 genomes]
rs13112009	1.00[ASN][1000 genomes]
rs13115289	0.82[ASN][1000 genomes]
rs13115416	0.92[ASN][1000 genomes]
rs13117741	0.86[ASN][1000 genomes]
rs13120233	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13120674	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13121471	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13123489	1.00[ASN][1000 genomes]
rs13129376	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134285	0.94[ASN][1000 genomes]
rs13134708	0.88[ASN][1000 genomes]
rs13138589	1.00[ASN][1000 genomes]
rs13145472	0.90[ASN][1000 genomes]
rs13147181	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13147327	1.00[ASN][1000 genomes]
rs13147530	1.00[ASN][1000 genomes]
rs13147729	0.88[ASN][1000 genomes]
rs13150274	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13150362	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1503616	0.95[ASN][1000 genomes]
rs1503618	0.91[ASN][1000 genomes]
rs1503619	0.91[ASN][1000 genomes]
rs1503622	0.83[ASN][1000 genomes]
rs1503628	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604723	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16997928	0.94[ASN][1000 genomes]
rs17011502	0.95[ASN][1000 genomes]
rs17011512	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011514	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011515	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011593	0.95[ASN][1000 genomes]
rs17011614	0.87[ASN][1000 genomes]
rs1847345	0.89[ASN][1000 genomes]
rs1955280	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995473	0.95[ASN][1000 genomes]
rs2391093	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2391100	0.83[ASN][1000 genomes]
rs2391101	1.00[ASN][1000 genomes]
rs34078351	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35119048	0.91[ASN][1000 genomes]
rs35815056	0.95[ASN][1000 genomes]
rs4295276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4373174	0.95[ASN][1000 genomes]
rs4413416	1.00[ASN][1000 genomes]
rs4833353	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833354	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834141	0.94[AFR][1000 genomes]
rs55832124	0.80[ASN][1000 genomes]
rs56807249	0.80[ASN][1000 genomes]
rs57858535	0.91[ASN][1000 genomes]
rs57921410	0.92[ASN][1000 genomes]
rs57945585	0.92[ASN][1000 genomes]
rs59049129	0.92[ASN][1000 genomes]
rs60076307	0.89[ASN][1000 genomes]
rs60726529	0.85[ASN][1000 genomes]
rs60860289	0.89[ASN][1000 genomes]
rs62322170	0.91[ASN][1000 genomes]
rs62322171	0.91[ASN][1000 genomes]
rs62322173	0.92[ASN][1000 genomes]
rs62322183	0.87[ASN][1000 genomes]
rs62322186	0.83[ASN][1000 genomes]
rs62322221	0.80[ASN][1000 genomes]
rs62324214	0.95[ASN][1000 genomes]
rs62324216	0.93[ASN][1000 genomes]
rs62324219	0.93[ASN][1000 genomes]
rs62324227	0.95[ASN][1000 genomes]
rs62324228	0.95[ASN][1000 genomes]
rs62324229	0.95[ASN][1000 genomes]
rs62324230	0.95[ASN][1000 genomes]
rs6534582	0.90[ASN][1000 genomes]
rs6811594	1.00[ASN][1000 genomes]
rs6839577	0.99[ASN][1000 genomes]
rs6857787	0.90[ASN][1000 genomes]
rs72674477	0.93[ASN][1000 genomes]
rs72674480	0.95[ASN][1000 genomes]
rs72675928	0.80[ASN][1000 genomes]
rs7660971	0.95[ASN][1000 genomes]
rs7661738	0.91[ASN][1000 genomes]
rs7664355	0.93[ASN][1000 genomes]
rs7665607	0.83[ASN][1000 genomes]
rs7688921	0.94[ASN][1000 genomes]
rs7695444	0.87[ASN][1000 genomes]
rs7696279	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012833	chr4:127468474-127760933	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv537242	chr4:127468474-127760933	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv524850	chr4:127470903-127768849	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1013854	chr4:127508969-127663216	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1009499	chr4:127532856-127659010	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv537243	chr4:127532856-127659010	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1007477	chr4:127561735-127726291	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv537244	chr4:127561735-127726291	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2752024	chr4:127584697-127671942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv595386	chr4:127597069-127668828	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1028609	chr4:127597319-127664629	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv879907	chr4:127646765-127709859	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	nsv879908	chr4:127646765-127749390	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	nsv879909	chr4:127646765-127792639	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv879910	chr4:127646765-127805466	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv879911	chr4:127646765-127835677	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1388240	PLK4	cis	cerebellum	SCAN
rs1388240	ABCA13	trans	cerebellum	SCAN
rs1388240	DAPK3	trans	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:127652800-127658000	Active TSS	K562	blood
2	chr4:127654800-127660000	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links