Variant report

Variant	rs10039801
Chromosome Location	chr5:93938691-93938692
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10035650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10037816	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041551	1.00[CHB][hapmap]
rs10043779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051931	1.00[CHB][hapmap]
rs10053484	1.00[CHB][hapmap]
rs10058618	1.00[CHB][hapmap]
rs10072760	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10076188	1.00[CHB][hapmap]
rs10078304	1.00[CHB][hapmap]
rs10476612	1.00[CHB][hapmap]
rs10476613	1.00[CHB][hapmap]
rs10476615	1.00[CHB][hapmap]
rs12517866	1.00[CHB][hapmap]
rs12518034	1.00[CHB][hapmap]
rs12522312	1.00[CHB][hapmap]
rs13358642	1.00[CHB][hapmap]
rs13361811	1.00[CHB][hapmap]
rs13362556	1.00[CHB][hapmap]
rs17083818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132547	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs306573	1.00[CHB][hapmap]
rs6873364	1.00[CHB][hapmap]
rs755898	1.00[CHB][hapmap]
rs7725095	1.00[CHB][hapmap]
rs7737779	1.00[CHB][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10039801	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs10039801	ANKRD32	cis	multi-tissue	Pritchard
rs10039801	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93934600-93942400	Weak transcription	Fetal Stomach	stomach
2	chr5:93934600-93951200	Weak transcription	Brain Anterior Caudate	brain
3	chr5:93935000-93940000	Weak transcription	Gastric	stomach
4	chr5:93936600-93939000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:93936800-93950000	Weak transcription	Hela-S3	cervix
6	chr5:93937200-93939400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr5:93937600-93939000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr5:93937800-93939000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr5:93937800-93944400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr5:93937800-93950800	Weak transcription	Brain Angular Gyrus	brain
11	chr5:93938000-93938800	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr5:93938200-93938800	Strong transcription	Ovary	ovary
13	chr5:93938400-93939800	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:93938400-93942400	Weak transcription	Aorta	Aorta
15	chr5:93938400-93951200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:93938600-93939200	Weak transcription	Fetal Lung	lung
17	chr5:93938600-93952400	Weak transcription	Primary T cells from cord blood	blood

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