Variant report

Variant	rs1861239
Chromosome Location	chr7:38515584-38515585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38510679..38513709-chr7:38513758..38517048,3	K562	blood:
2	chr7:38510679..38513066-chr7:38514460..38517048,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10951558	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12154302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12673437	1.00[GIH][hapmap]
rs1558617	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171359	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17171367	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17171377	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17171384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171387	0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs17498899	1.00[CEU][hapmap]
rs17499670	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs17506922	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2299949	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2893561	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs34057414	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3735089	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778876	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3778879	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778882	1.00[CEU][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3778887	0.82[JPT][hapmap]
rs3807413	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3807416	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3807419	0.93[ASN][1000 genomes]
rs3807425	0.87[JPT][hapmap]
rs3823591	1.00[GIH][hapmap];0.80[MKK][hapmap]
rs3823594	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs3823598	0.82[JPT][hapmap]
rs3943706	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs41279585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953928	0.82[JPT][hapmap]
rs6956760	0.85[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.86[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	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv830965	chr7:38350614-38521047	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1861239	AMPH	cis	Nerve Tibial	GTEx
rs1861239	AMPH	cis	Adipose Subcutaneous	GTEx
rs1861239	SFRP4	cis	cerebellum	SCAN
rs1861239	AMPH	cis	Muscle Skeletal	GTEx
rs1861239	AMPH	cis	Skin Sun Exposed Lower leg	GTEx
rs1861239	AMPH	cis	normal skin	skin_eQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38499800-38523600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:38501000-38522400	Weak transcription	Fetal Muscle Leg	muscle
3	chr7:38501800-38522600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:38502600-38549400	Weak transcription	Fetal Stomach	stomach
5	chr7:38502800-38533800	Weak transcription	Aorta	Aorta
6	chr7:38503800-38522400	Weak transcription	Fetal Lung	lung
7	chr7:38512200-38516400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:38513600-38515800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:38513600-38516800	Weak transcription	Fetal Brain Male	brain
10	chr7:38514600-38516000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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