Variant report

Variant	rs10900384
Chromosome Location	chr1:146501348-146501349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:144889740..144892703-chr1:146500075..146502138,3	MCF-7	breast:
2	chr1:146500274..146502846-chr1:146563478..146565211,2	MCF-7	breast:
3	chr1:144890884..144894068-chr1:146500995..146504405,3	K562	blood:
4	chr1:146500874..146503757-chr1:146554554..146557584,3	K562	blood:
5	chr1:146500894..146503604-chr1:146505375..146507725,2	MCF-7	breast:
6	chr1:146500715..146505145-chr1:146554885..146558544,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230832	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10218707	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs11240094	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11808402	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11809158	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12122453	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12122534	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12123494	0.82[AMR][1000 genomes]
rs12139768	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12141387	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12142744	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12742988	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1925343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1984615	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2031481	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap]
rs3862922	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4950330	0.98[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4950332	0.90[CHB][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs517201	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs524016	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs604716	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs614763	0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs6665804	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	nsv428224	chr1:145613243-146553918	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv2757753	chr1:145883119-146697542	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv946295	chr1:146471863-146507583	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
6	nsv872253	chr1:146494246-146548549	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10900384	RP11-94I2.1	cis	lung	GTEx
rs10900384	RP11-325P15.1	cis	lung	GTEx
rs10900384	NBPF13P	cis	lung	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146494800-146504200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:146501000-146502600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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