Variant report

Variant	rs4237544
Chromosome Location	chr11:47454271-47454272
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47453415..47456321-chr11:47460580..47462674,2	K562	blood:

Variant related genes	Relation type
ENSG00000252327	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1044269	0.92[GIH][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10742805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742806	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10742816	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs10769267	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11819955	0.93[JPT][hapmap]
rs11820650	0.82[ASN][1000 genomes]
rs11820680	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11821917	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11824864	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11827106	0.80[ASN][1000 genomes]
rs11828339	0.92[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12282783	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12419342	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1474056	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs17198158	0.92[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs17790804	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2138767	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs2242511	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs3740684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3740685	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781628	0.82[ASN][1000 genomes]
rs3824867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3847503	0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4147730	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs4282946	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4384349	0.80[ASN][1000 genomes]
rs4752783	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs4752786	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs4752829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752836	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752839	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs4752843	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs4752992	0.82[ASN][1000 genomes]
rs60380053	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60882887	0.84[ASN][1000 genomes]
rs61000762	0.84[ASN][1000 genomes]
rs7101772	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7104366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7105122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7105907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107853	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7108143	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7111873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119556	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7125468	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7126210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7130693	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753812	0.92[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7931089	0.92[JPT][hapmap]
rs7948705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9666924	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs9734013	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919526	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
6	nsv975328	chr11:47446815-47471052	Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4237544	FAM92A3	trans	cerebellum	SCAN
rs4237544	PSMC3	cis	cerebellum	SCAN
rs4237544	MADD	cis	parietal	SCAN
rs4237544	PTPRJ	cis	parietal	SCAN
rs4237544	MDK	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47459600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:47448800-47454800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr11:47449000-47454800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr11:47449000-47454800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:47449000-47454800	Weak transcription	HSMM	muscle
7	chr11:47449000-47457200	Weak transcription	Right Atrium	heart
8	chr11:47449000-47459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:47449000-47459400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:47449800-47454800	Weak transcription	Fetal Muscle Leg	muscle
11	chr11:47449800-47454800	Weak transcription	HSMMtube	muscle
12	chr11:47452400-47454600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:47452400-47455000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:47453200-47454600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:47453400-47458800	Enhancers	HepG2	liver
16	chr11:47453400-47469200	Weak transcription	Psoas Muscle	Psoas
17	chr11:47453400-47480000	Weak transcription	Thymus	Thymus
18	chr11:47453600-47454800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:47453600-47459000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr11:47454000-47455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr11:47454200-47454600	Weak transcription	Liver	Liver

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