Variant report

Variant	rs7802098
Chromosome Location	chr7:47862994-47862995
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:29)

rs_ID	r²[population]
rs10429127	0.90[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12702393	0.80[CEU][hapmap];0.87[TSI][hapmap]
rs12702395	1.00[JPT][hapmap]
rs13231277	0.87[TSI][hapmap]
rs13241400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13246591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13247692	0.90[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs13247756	0.94[EUR][1000 genomes]
rs17131825	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17131827	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17131855	0.94[EUR][1000 genomes]
rs17545682	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1851403	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs2053985	0.81[MEX][hapmap]
rs2123610	0.94[EUR][1000 genomes]
rs34069037	0.96[EUR][1000 genomes]
rs34703899	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34712849	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35781192	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4391316	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66733202	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66755489	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67572268	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6947342	1.00[JPT][hapmap]
rs6950328	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6962855	1.00[JPT][hapmap]
rs73103467	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7780916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7788583	0.83[CEU][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7802098	TMED4	cis	parietal	SCAN
rs7802098	UPP1	cis	cerebellum	SCAN
rs7802098	SNORA5C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47852800-47879000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:47855000-47869600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:47855000-47880200	Weak transcription	Lung	lung
4	chr7:47855800-47866800	Weak transcription	Left Ventricle	heart
5	chr7:47855800-47902400	Weak transcription	Adipose Nuclei	Adipose
6	chr7:47859000-47866400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:47859000-47866600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:47859000-47869000	Weak transcription	HSMM	muscle
9	chr7:47859400-47866400	Weak transcription	HSMMtube	muscle

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