Variant report

Variant	rs368043
Chromosome Location	chr7:138002082-138002083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1035329	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11536612	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12707380	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1691717	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs357370	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs357374	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs357375	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs357380	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs357387	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs357405	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs357410	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs357413	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs357415	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs357416	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs357417	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs357419	0.94[EUR][1000 genomes]
rs357420	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs357433	0.83[EUR][1000 genomes]
rs357434	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs357436	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs357439	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs357442	0.83[EUR][1000 genomes]
rs357444	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs357452	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs357453	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs357455	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs368370	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs373089	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs376305	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs378745	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs386059	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs396783	0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs401454	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs402615	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs403675	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs407702	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs409365	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs410156	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs410187	1.00[ASW][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs414919	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs424197	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs424335	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs424847	1.00[ASW][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs443184	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831152	chr7:137884311-138033117	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1029101	chr7:137952620-138005671	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv5967	chr7:137988239-138015844	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv499698	chr7:137991842-138004097	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs368043	CLEC5A	cis	cerebellum	SCAN
rs368043	C7orf49	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137995200-138012000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:137998600-138002400	Enhancers	Fetal Intestine Large	intestine
3	chr7:138000400-138002200	Enhancers	Fetal Intestine Small	intestine
4	chr7:138001400-138005200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr7:138001600-138002200	Flanking Active TSS	HepG2	liver

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