Variant report

Variant	rs9400672
Chromosome Location	chr6:114096407-114096408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1026635	0.82[ASN][1000 genomes]
rs1026636	0.82[ASN][1000 genomes]
rs1026640	0.82[ASN][1000 genomes]
rs1031797	0.81[ASN][1000 genomes]
rs1031798	0.81[ASN][1000 genomes]
rs13209042	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs1564063	0.81[ASN][1000 genomes]
rs1585564	0.82[ASN][1000 genomes]
rs17075611	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2018090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126461	0.81[ASN][1000 genomes]
rs2126462	0.81[ASN][1000 genomes]
rs2615508	0.80[ASN][1000 genomes]
rs2615518	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2615529	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2615530	0.81[ASN][1000 genomes]
rs2615531	0.81[ASN][1000 genomes]
rs2615532	0.81[ASN][1000 genomes]
rs2615533	0.82[ASN][1000 genomes]
rs2695451	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2695452	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2753884	0.81[ASN][1000 genomes]
rs2810179	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs2810182	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2810187	0.82[ASN][1000 genomes]
rs2810188	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2810189	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2810191	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2810195	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2810196	0.81[ASN][1000 genomes]
rs34777588	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4574672	0.87[ASN][1000 genomes]
rs4945503	0.81[ASN][1000 genomes]
rs55705700	0.81[ASN][1000 genomes]
rs6568807	0.87[ASN][1000 genomes]
rs6918103	0.86[ASN][1000 genomes]
rs6923574	0.86[ASN][1000 genomes]
rs6940434	0.86[ASN][1000 genomes]
rs773685	0.95[JPT][hapmap]
rs7752266	0.83[ASN][1000 genomes]
rs7760821	0.86[ASN][1000 genomes]
rs7765004	0.86[ASN][1000 genomes]
rs9372374	0.85[ASN][1000 genomes]
rs9372376	0.84[ASN][1000 genomes]
rs9374426	0.86[ASN][1000 genomes]
rs9374429	0.81[ASN][1000 genomes]
rs9384882	0.86[ASN][1000 genomes]
rs9387174	0.86[ASN][1000 genomes]
rs9387176	0.86[ASN][1000 genomes]
rs9387177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9387179	0.82[ASN][1000 genomes]
rs9398364	0.81[ASN][1000 genomes]
rs9400667	0.86[ASN][1000 genomes]
rs9400671	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400676	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs949599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959211	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs963884	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[ASN][1000 genomes]

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	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv464023	chr6:114071720-114114057	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	nsv604532	chr6:114071720-114114057	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9400672	REV3L	cis	parietal	SCAN
rs9400672	RWDD1	cis	cerebellum	SCAN
rs9400672	KDM4D	trans	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114085400-114098000	Weak transcription	Stomach Mucosa	stomach
2	chr6:114094000-114096600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:114094000-114098800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:114096200-114097800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:114096200-114098000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:114096200-114098200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:114096200-114098200	Weak transcription	Fetal Lung	lung

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