Variant report

Variant	rs6956760
Chromosome Location	chr7:38537898-38537899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12154302	0.84[ASN][1000 genomes]
rs13239504	0.86[AFR][1000 genomes]
rs1558617	0.86[ASN][1000 genomes]
rs17171367	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs17171377	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs17171384	0.85[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs17171387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861239	0.85[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2267808	0.82[JPT][hapmap]
rs2299949	0.93[JPT][hapmap]
rs2893561	0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34433569	0.88[AFR][1000 genomes]
rs34523382	0.88[AFR][1000 genomes]
rs34665148	0.88[AFR][1000 genomes]
rs34789395	0.95[AFR][1000 genomes]
rs35367242	0.88[AFR][1000 genomes]
rs35375449	0.95[AFR][1000 genomes]
rs35440398	0.93[AFR][1000 genomes]
rs35978695	0.86[AFR][1000 genomes]
rs3735089	0.85[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs3778876	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778879	0.85[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs3807413	0.93[JPT][hapmap]
rs3807416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3807425	0.81[JPT][hapmap]
rs3807426	0.82[JPT][hapmap]
rs3823594	1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3943706	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs41279585	0.86[ASN][1000 genomes]
rs66520224	0.95[AFR][1000 genomes]
rs7811601	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6956760	AMPH	cis	normal skin	skin_eQTL
rs6956760	AMPH	cis	Skin Sun Exposed Lower leg	GTEx
rs6956760	VPS41	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38502600-38549400	Weak transcription	Fetal Stomach	stomach
2	chr7:38524000-38543400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:38524200-38545000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:38528600-38553000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:38531400-38544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:38531800-38543800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr7:38532000-38540200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:38533200-38542800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr7:38534200-38542400	Weak transcription	Aorta	Aorta

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