Variant report

Variant	rs970257
Chromosome Location	chr10:29237182-29237183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:29228534..29232701-chr10:29236667..29238298,3	MCF-7	breast:
2	chr10:28965152..28968050-chr10:29236571..29238763,2	K562	blood:
3	chr10:29236808..29238551-chr10:29250503..29252839,2	MCF-7	breast:
4	chr10:29205443..29207761-chr10:29235402..29237330,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000095739	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11007321	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539443	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1578618	0.80[ASN][1000 genomes]
rs1624345	0.91[ASN][1000 genomes]
rs1691910	0.91[ASN][1000 genomes]
rs1691915	0.91[ASN][1000 genomes]
rs1691917	0.91[ASN][1000 genomes]
rs1691928	0.91[ASN][1000 genomes]
rs1832844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1908573	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132322	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2132323	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2453618	0.91[ASN][1000 genomes]
rs3947425	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4749364	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4749368	0.84[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4749369	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs703041	1.00[ASN][1000 genomes]
rs787355	1.00[ASN][1000 genomes]
rs788066	1.00[JPT][hapmap]
rs7894551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897902	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs805198	0.82[ASN][1000 genomes]
rs813111	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1043820	chr10:29172894-29259450	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1040780	chr10:29172894-29260154	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs970257	LYZL1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:29234400-29237200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr10:29235200-29237400	Enhancers	Muscle Satellite Cultured Cells	--
3	chr10:29235200-29237400	Enhancers	Osteobl	bone
4	chr10:29235600-29237600	Weak transcription	A549	lung
5	chr10:29235600-29238000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:29236000-29237400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:29236000-29248800	Weak transcription	Fetal Heart	heart
8	chr10:29236200-29237600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr10:29236400-29238600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:29236600-29238400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr10:29236600-29238600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr10:29237000-29239400	Enhancers	HepG2	liver

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