Variant report

Variant	rs3003376
Chromosome Location	chr1:10071301-10071302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11121510	0.84[AFR][1000 genomes]
rs11121512	0.84[ASN][1000 genomes]
rs11121514	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12140058	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1220420	0.82[ASN][1000 genomes]
rs1220421	0.92[CEU][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs1234694	0.87[ASW][hapmap];0.84[CEU][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.80[MEX][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap];0.80[ASN][1000 genomes]
rs1660733	0.92[CEU][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2890358	0.93[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3003377	0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3003378	0.93[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3013788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3123522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762290	0.81[ASW][hapmap];0.92[LWK][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap]
rs58528460	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6541073	0.92[CEU][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6541075	0.84[EUR][1000 genomes]
rs6661806	0.84[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6664631	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6671289	0.81[ASW][hapmap];0.80[MKK][hapmap];0.82[YRI][hapmap]
rs6678023	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6693449	0.83[EUR][1000 genomes]
rs6696978	0.82[YRI][hapmap]
rs7517360	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7517806	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517812	0.81[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs7528979	0.87[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7539191	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7539725	0.81[GIH][hapmap]
rs9919194	0.83[AFR][1000 genomes];0.82[EUR][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	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3003376	LZIC	cis	multi-tissue	Pritchard
rs3003376	PIK3CD	cis	cerebellum	SCAN
rs3003376	HES3	cis	cerebellum	SCAN
rs3003376	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs3003376	LZIC	cis	lymphoblastoid	seeQTL
rs3003376	LZIC	cis	Lymphoblastoid	GTEx
rs3003376	MTHFR	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10059200-10075000	Weak transcription	Fetal Heart	heart
2	chr1:10061600-10077000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:10061800-10077200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:10068000-10075600	Weak transcription	Left Ventricle	heart
5	chr1:10070200-10071400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:10071000-10071800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr1:10071000-10071800	Strong transcription	Adipose Nuclei	Adipose
8	chr1:10071200-10076400	Strong transcription	Primary monocytes fromperipheralblood	blood

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