Variant report

Variant	rs346697
Chromosome Location	chr1:45545002-45545003
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11211074	0.97[ASN][1000 genomes]
rs1144868	0.98[ASN][1000 genomes]
rs11806438	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810239	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1226670	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226733	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1226734	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1226735	0.83[ASN][1000 genomes]
rs1226746	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226747	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226748	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226836	0.86[ASN][1000 genomes]
rs1226914	0.97[ASN][1000 genomes]
rs13374935	0.80[EUR][1000 genomes]
rs1782459	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938300	0.98[ASN][1000 genomes]
rs1938301	0.98[ASN][1000 genomes]
rs1938303	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938304	0.98[ASN][1000 genomes]
rs2088956	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2105458	1.00[ASN][1000 genomes]
rs2202152	0.83[AMR][1000 genomes]
rs2356302	0.98[ASN][1000 genomes]
rs238249	1.00[ASN][1000 genomes]
rs2997461	1.00[ASN][1000 genomes]
rs2997465	0.98[ASN][1000 genomes]
rs3009968	0.98[ASN][1000 genomes]
rs3009969	0.98[ASN][1000 genomes]
rs3009974	1.00[ASN][1000 genomes]
rs3009979	1.00[ASN][1000 genomes]
rs34134455	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346684	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346687	0.98[ASN][1000 genomes]
rs346693	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346695	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346696	0.98[ASN][1000 genomes]
rs346698	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346700	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346701	1.00[ASN][1000 genomes]
rs346702	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346705	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346706	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346707	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346708	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346712	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346716	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346717	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346719	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346721	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346723	0.98[ASN][1000 genomes]
rs346724	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346729	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346731	0.97[ASN][1000 genomes]
rs346732	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346733	1.00[ASN][1000 genomes]
rs346734	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346735	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346736	1.00[ASN][1000 genomes]
rs346737	0.98[ASN][1000 genomes]
rs368393	0.89[EUR][1000 genomes]
rs3738246	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3850855	0.98[ASN][1000 genomes]
rs3850856	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415536	1.00[ASN][1000 genomes]
rs4454584	0.82[ASN][1000 genomes]
rs454624	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660295	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660834	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4660839	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660841	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932948	0.80[ASN][1000 genomes]
rs56086213	0.80[ASN][1000 genomes]
rs56363452	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56791336	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57754814	0.80[ASN][1000 genomes]
rs58374842	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58934647	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59220391	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61789780	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789781	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789815	0.80[EUR][1000 genomes]
rs6429557	0.98[ASN][1000 genomes]
rs6688318	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6702327	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72684493	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974143	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv945917	chr1:45533650-45546555	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45525800-45558600	Weak transcription	HepG2	liver
2	chr1:45541000-45546800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:45543400-45555400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:45543600-45546800	ZNF genes & repeats	Fetal Brain Female	brain
5	chr1:45543800-45562200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:45544200-45545800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:45544200-45545800	ZNF genes & repeats	Fetal Stomach	stomach
8	chr1:45544200-45546600	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr1:45544200-45546800	ZNF genes & repeats	Brain Germinal Matrix	brain
10	chr1:45544400-45549200	Weak transcription	Gastric	stomach
11	chr1:45544400-45550000	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:45544400-45560200	Weak transcription	Pancreas	Pancrea
13	chr1:45544600-45552000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:45545000-45545400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:45545000-45545400	Bivalent/Poised TSS	K562	blood
16	chr1:45545000-45546000	Strong transcription	Ovary	ovary
17	chr1:45545000-45558200	Weak transcription	Duodenum Mucosa	Duodenum

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