Variant report

Variant	rs10250246
Chromosome Location	chr7:40728868-40728869
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	chr7:40726572..40729922-chr7:40745740..40747693,3	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10280713	0.91[CEU][hapmap]
rs10486813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951638	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1146040	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1203725	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1203726	0.86[ASN][1000 genomes]
rs1203727	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1203728	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203730	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1203733	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1203734	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1203739	0.82[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs12701825	0.91[CEU][hapmap]
rs12701826	0.91[CEU][hapmap]
rs13235741	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13239043	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs17171762	0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs17171763	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171764	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17528582	0.82[GIH][hapmap]
rs1811209	0.95[CEU][hapmap]
rs1921750	0.86[ASN][1000 genomes]
rs2011636	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35428147	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4050983	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs57655172	0.87[ASN][1000 genomes]
rs62451217	0.86[ASN][1000 genomes]
rs62451219	0.90[ASN][1000 genomes]
rs6462987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947078	0.91[CEU][hapmap]
rs6952969	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6957725	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs6958129	0.91[CEU][hapmap]
rs6959899	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs6965055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978898	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73310278	0.90[ASN][1000 genomes]
rs73310281	0.89[ASN][1000 genomes]
rs7808606	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv887987	chr7:40505382-40748650	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1025605	chr7:40623026-40789063	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538823	chr7:40623026-40789063	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1019833	chr7:40649369-40767377	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv538824	chr7:40649369-40767377	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv887988	chr7:40685811-40782572	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10250246	GAS2	trans	lymphoblastoid	seeQTL
rs10250246	STEAP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40723200-40737200	Weak transcription	Osteobl	bone
2	chr7:40723600-40737400	Weak transcription	HSMM	muscle
3	chr7:40723800-40733600	Weak transcription	Aorta	Aorta
4	chr7:40724000-40733400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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