Variant report

Variant	rs10753796
Chromosome Location	chr1:169757487-169757488
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169751349..169757764-chr1:169760418..169766538,11	K562	blood:
2	chr1:169751762..169754671-chr1:169756355..169758348,3	K562	blood:
3	chr1:169753568..169755601-chr1:169755944..169758258,2	MCF-7	breast:
4	chr1:169755971..169761352-chr1:169761713..169764832,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10157246	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10157266	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs10489177	0.93[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10753794	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10753795	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs10800477	0.93[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10919236	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10919237	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10919238	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10919240	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10919242	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10919243	0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11588275	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12035144	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12049325	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs12128754	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs12129417	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12135656	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs12404614	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12760433	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs2205845	0.82[CEU][hapmap]
rs2420507	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3753311	0.89[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap]
rs6427216	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs6427219	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6670253	0.82[ASN][1000 genomes]
rs6676623	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6676718	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6683782	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6686522	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6696884	0.82[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6701718	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs722511	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7552710	0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs882595	0.93[CHB][hapmap];0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats 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	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10753796	SCYL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169749400-169761400	Weak transcription	Liver	Liver
2	chr1:169750800-169762800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:169751600-169760200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:169751600-169762600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:169752600-169760200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:169753600-169763000	Weak transcription	HMEC	breast
7	chr1:169754400-169760800	Weak transcription	Dnd41	blood
8	chr1:169755000-169760000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:169756400-169761000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:169756400-169762400	Weak transcription	Fetal Brain Male	brain
11	chr1:169756600-169762600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:169757000-169762400	Weak transcription	Fetal Thymus	thymus
13	chr1:169757200-169758400	Enhancers	HepG2	liver
14	chr1:169757400-169763000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:169757400-169763000	Weak transcription	Thymus	Thymus
16	chr1:169757400-169763200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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