Variant report

Variant	rs3003378
Chromosome Location	chr1:10063098-10063099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10061638..10064591-chr1:10064768..10066310,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10779734	0.86[ASN][1000 genomes]
rs11121510	0.82[ASN][1000 genomes]
rs11121512	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11121514	0.81[ASN][1000 genomes]
rs11828	0.87[ASN][1000 genomes]
rs12140009	0.86[ASN][1000 genomes]
rs12140015	0.86[ASN][1000 genomes]
rs12140058	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1220389	0.83[ASN][1000 genomes]
rs1220399	0.87[ASN][1000 genomes]
rs1220400	0.84[ASN][1000 genomes]
rs1220402	0.84[ASN][1000 genomes]
rs1220420	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1220421	0.85[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1220424	0.84[ASN][1000 genomes]
rs1234694	0.81[ASW][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1628143	0.86[ASN][1000 genomes]
rs1660733	0.85[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2890358	0.87[ASW][hapmap];0.85[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2919694	0.81[ASN][1000 genomes]
rs3003376	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]
rs3003377	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3013783	0.81[ASN][1000 genomes]
rs3013784	0.87[ASN][1000 genomes]
rs3013788	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3123522	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3762290	0.87[ASW][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap]
rs58528460	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6541073	0.85[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6661806	0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6664631	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6671289	0.87[ASW][hapmap];0.90[MKK][hapmap]
rs6678023	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6680076	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7517360	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7517806	0.91[ASN][1000 genomes]
rs7517812	0.86[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7528979	0.93[ASW][hapmap];0.93[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs7539191	0.97[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3003378	LZIC	cis	multi-tissue	Pritchard
rs3003378	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 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	chr1:10061800-10067800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:10061800-10077200	Weak transcription	Brain Substantia Nigra	brain
5	chr1:10063000-10067400	Weak transcription	Monocytes-CD14+_RO01746	blood

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