Variant report

Variant	rs6786853
Chromosome Location	chr3:100310812-100310813
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10428254	0.94[ASN][1000 genomes]
rs10511187	0.95[ASN][1000 genomes]
rs10511188	0.95[ASN][1000 genomes]
rs10936264	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10936276	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs1165521	0.89[ASN][1000 genomes]
rs11923487	0.83[ASN][1000 genomes]
rs12634935	0.95[ASN][1000 genomes]
rs12635503	0.95[ASN][1000 genomes]
rs12636790	0.95[ASN][1000 genomes]
rs12637319	0.95[ASN][1000 genomes]
rs1305373	0.95[ASN][1000 genomes]
rs1305375	0.95[ASN][1000 genomes]
rs13069547	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13321761	0.95[ASN][1000 genomes]
rs1471375	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs1520650	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs1531772	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs1676340	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs16842463	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs1718275	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs1842732	0.93[ASN][1000 genomes]
rs2169554	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460719	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4129205	0.85[CEU][hapmap];0.83[CHB][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs57404153	0.83[ASN][1000 genomes]
rs58618663	0.85[ASN][1000 genomes]
rs60151360	0.94[ASN][1000 genomes]
rs61549238	0.87[ASN][1000 genomes]
rs619149	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs653530	0.95[ASN][1000 genomes]
rs661266	0.95[ASN][1000 genomes]
rs6763638	0.93[ASW][hapmap];0.85[CEU][hapmap];0.89[CHD][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs6768258	0.95[ASN][1000 genomes]
rs6770693	0.95[ASN][1000 genomes]
rs6771421	0.95[ASN][1000 genomes]
rs6773148	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6783630	0.95[ASN][1000 genomes]
rs6785969	0.95[ASN][1000 genomes]
rs73141183	0.88[ASN][1000 genomes]
rs7426414	0.87[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs7426462	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7427360	0.83[ASN][1000 genomes]
rs7429915	0.93[ASW][hapmap];0.85[CEU][hapmap];0.89[CHD][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap]
rs7432710	0.81[CEU][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs7433875	0.83[ASN][1000 genomes]
rs7611100	0.82[CEU][hapmap];0.87[CHD][hapmap]
rs7617909	0.83[ASN][1000 genomes]
rs900235	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs9290097	0.94[ASN][1000 genomes]
rs9290098	0.95[ASN][1000 genomes]
rs9290099	0.95[ASN][1000 genomes]
rs9290100	0.95[ASN][1000 genomes]
rs9790050	0.95[ASN][1000 genomes]
rs9790137	0.95[ASN][1000 genomes]
rs9790219	0.95[ASN][1000 genomes]
rs9818800	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825818	0.83[ASN][1000 genomes]
rs9829641	0.94[ASN][1000 genomes]
rs9829972	0.93[ASN][1000 genomes]
rs9834474	0.94[ASN][1000 genomes]
rs9834776	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9838918	0.94[ASN][1000 genomes]
rs9853434	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856061	0.94[ASN][1000 genomes]
rs9856338	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9860005	0.95[ASN][1000 genomes]
rs9874401	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751965	chr3:100299310-100462527	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	esv2751966	chr3:100299310-100468500	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2756284	chr3:100299329-100427937	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2752830	chr3:100299329-100442478	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv432464	chr3:100299329-100442478	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv2751967	chr3:100299329-100455139	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv2751968	chr3:100299329-100476713	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv432466	chr3:100299329-100476713	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv536667	chr3:100308355-100445857	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv460770	chr3:100310812-100433592	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv591150	chr3:100310812-100433592	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6786853	IMPG2	cis	cerebellum	SCAN
rs6786853	TMEM45A	cis	parietal	SCAN
rs6786853	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs6786853	OR5K4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100308800-100312000	Enhancers	Fetal Intestine Large	intestine
2	chr3:100309200-100311000	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr3:100309200-100312000	Enhancers	Fetal Intestine Small	intestine
4	chr3:100309600-100311000	Enhancers	A549	lung
5	chr3:100310200-100311000	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr3:100310800-100311600	Enhancers	Liver	Liver
7	chr3:100310800-100319200	Weak transcription	Duodenum Mucosa	Duodenum

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