Variant report

Variant	rs1031389
Chromosome Location	chr5:93918392-93918393
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	chr5:93917068..93919147-chr5:93934324..93935876,2	K562	blood:

Extended variants
information (count: 114 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10037940	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs10039797	0.82[AMR][1000 genomes]
rs10052066	0.93[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs10062402	0.84[AMR][1000 genomes]
rs1006626	0.86[ASN][1000 genomes]
rs10072894	0.93[CEU][hapmap];0.85[AMR][1000 genomes]
rs10074178	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10078522	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs10476614	0.92[CEU][hapmap];0.84[AMR][1000 genomes]
rs11135406	0.90[CHB][hapmap]
rs11135407	0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs11135408	0.87[ASN][1000 genomes]
rs11135410	0.80[CHB][hapmap]
rs1124667	0.93[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes]
rs1124668	0.90[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs11948061	0.80[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs12189060	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs12514098	0.81[CHD][hapmap]
rs12515845	0.90[CHB][hapmap]
rs12519472	0.89[CHB][hapmap]
rs12523457	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs12652705	0.85[ASN][1000 genomes]
rs12653819	0.90[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs12654602	0.87[ASN][1000 genomes]
rs12655521	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs12655665	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs12655669	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs12656300	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12656694	0.87[ASN][1000 genomes]
rs12657227	0.86[ASN][1000 genomes]
rs12657323	0.87[ASN][1000 genomes]
rs12659597	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs1390642	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs1390644	0.84[ASN][1000 genomes]
rs1451734	0.92[CEU][hapmap];0.84[AMR][1000 genomes]
rs1451735	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs1549179	0.92[CEU][hapmap];0.84[AMR][1000 genomes]
rs1562911	0.90[CHB][hapmap]
rs17083824	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs17083827	0.87[ASN][1000 genomes]
rs17083828	0.87[ASN][1000 genomes]
rs17083873	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs17083887	0.85[ASN][1000 genomes]
rs17083888	0.84[ASN][1000 genomes]
rs17083896	0.90[CHB][hapmap]
rs17083911	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs17083945	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs2032813	0.84[ASN][1000 genomes]
rs2044911	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs2047318	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs2047319	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs2112449	0.93[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs2112450	0.80[MEX][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs2122984	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs2122985	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs2132548	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs2201620	0.83[ASN][1000 genomes]
rs2220965	0.84[ASN][1000 genomes]
rs2270626	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs2638	0.81[TSI][hapmap]
rs306574	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs421521	0.91[CEU][hapmap]
rs56242961	0.87[ASN][1000 genomes]
rs56824518	0.85[ASN][1000 genomes]
rs57188935	0.87[ASN][1000 genomes]
rs60191000	0.85[ASN][1000 genomes]
rs6556849	0.85[AMR][1000 genomes]
rs6556850	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs6556851	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs66464936	0.85[ASN][1000 genomes]
rs66483218	0.85[ASN][1000 genomes]
rs66488253	0.87[ASN][1000 genomes]
rs66518525	0.86[ASN][1000 genomes]
rs66578784	0.87[ASN][1000 genomes]
rs66694903	0.87[ASN][1000 genomes]
rs66696350	0.86[ASN][1000 genomes]
rs66936860	0.87[ASN][1000 genomes]
rs67313609	0.86[ASN][1000 genomes]
rs67531524	0.87[ASN][1000 genomes]
rs67831380	0.86[ASN][1000 genomes]
rs67994891	0.86[ASN][1000 genomes]
rs6869588	0.90[CHB][hapmap]
rs6879384	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs6883128	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs6883326	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs6890092	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs6891545	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs6897550	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs72771700	0.81[ASN][1000 genomes]
rs72773504	0.81[ASN][1000 genomes]
rs72773507	0.81[ASN][1000 genomes]
rs72773517	0.87[ASN][1000 genomes]
rs72773526	0.87[ASN][1000 genomes]
rs72773528	0.82[ASN][1000 genomes]
rs72773533	0.86[ASN][1000 genomes]
rs72773547	0.86[ASN][1000 genomes]
rs72773549	0.85[ASN][1000 genomes]
rs73136312	0.87[ASN][1000 genomes]
rs7446179	0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs747880	0.81[AMR][1000 genomes]
rs755899	0.82[AMR][1000 genomes]
rs755900	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs7709494	0.93[CEU][hapmap];0.82[AMR][1000 genomes]
rs7735473	0.81[CHB][hapmap]
rs7735659	0.86[ASN][1000 genomes]
rs7735924	0.80[MEX][hapmap]
rs7737187	0.82[CHB][hapmap]
rs9791082	0.90[CHB][hapmap];0.81[CHD][hapmap]

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	nsv1023191	chr5:93351646-93947928	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv537808	chr5:93351646-93947928	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2758002	chr5:93765205-94042201	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	esv2759354	chr5:93765205-94042201	Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv534495	chr5:93789736-93962131	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv598952	chr5:93823951-93956986	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1031389	MCTP1	cis	uninvolved skin	skin_eQTL
rs1031389	C5orf36	cis	cerebellum	SCAN
rs1031389	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs1031389	ANKRD32	cis	cerebellum	SCAN
rs1031389	LIX1	cis	parietal	SCAN
rs1031389	MCTP1	cis	Temporal Cortex	GTEx
rs1031389	MCTP1	cis	lymphoblastoid	seeQTL
rs1031389	MCTP1	cis	Cerebellum	GTEx
rs1031389	MCTP1	cis	normal skin	skin_eQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93903000-93919800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:93909800-93918800	Weak transcription	Pancreas	Pancrea
3	chr5:93914200-93918800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:93914600-93920200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:93917000-93918400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:93918000-93919000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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