Variant report

Variant	rs346707
Chromosome Location	chr1:45548254-45548255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs11211074	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1144868	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11806438	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810239	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1226670	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226733	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1226734	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1226735	0.83[ASN][1000 genomes]
rs1226746	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226747	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226748	0.86[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	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs1612575	1.00[CHD][hapmap]
rs1782459	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938300	0.98[ASN][1000 genomes]
rs1938301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1938303	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938304	0.98[ASN][1000 genomes]
rs2088956	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2105458	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2186219	0.91[JPT][hapmap]
rs2202152	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap]
rs2228084	0.91[CHD][hapmap]
rs2356302	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs238249	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2997461	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2997465	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3009968	0.98[ASN][1000 genomes]
rs3009969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3009974	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3009979	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3121732	0.91[JPT][hapmap]
rs34134455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346687	0.98[ASN][1000 genomes]
rs346693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346695	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346696	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs346697	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346698	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346700	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346701	1.00[ASN][1000 genomes]
rs346702	0.93[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346703	1.00[CHD][hapmap]
rs346705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346708	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346712	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346716	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346721	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346723	0.98[ASN][1000 genomes]
rs346724	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346725	1.00[CHD][hapmap]
rs346729	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346731	0.97[ASN][1000 genomes]
rs346732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346733	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs346734	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346735	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346736	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs346737	0.98[ASN][1000 genomes]
rs365108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs368393	0.90[EUR][1000 genomes]
rs3738246	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3850855	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3850856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415536	1.00[ASN][1000 genomes]
rs4454584	0.82[ASN][1000 genomes]
rs454624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660295	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660834	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4660839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55932948	0.80[ASN][1000 genomes]
rs56086213	0.80[ASN][1000 genomes]
rs56363452	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56791336	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57754814	0.80[ASN][1000 genomes]
rs58374842	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58934647	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59220391	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61789780	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789781	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6688318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6702327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72684493	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528534	0.80[CHD][hapmap]
rs974143	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs346707	NSUN4	cis	cerebellum	SCAN
rs346707	TIE1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45525800-45558600	Weak transcription	HepG2	liver
2	chr1:45543400-45555400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:45543800-45562200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:45544400-45549200	Weak transcription	Gastric	stomach
5	chr1:45544400-45550000	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:45544400-45560200	Weak transcription	Pancreas	Pancrea
7	chr1:45544600-45552000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:45545000-45558200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:45545800-45551400	Weak transcription	Fetal Stomach	stomach
10	chr1:45545800-45552000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:45546000-45549400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:45546000-45550600	Weak transcription	Aorta	Aorta
13	chr1:45546000-45554800	Weak transcription	Ovary	ovary
14	chr1:45546600-45550400	Weak transcription	Fetal Intestine Small	intestine
15	chr1:45546800-45548400	Weak transcription	Brain Germinal Matrix	brain
16	chr1:45546800-45555000	Weak transcription	Fetal Brain Female	brain
17	chr1:45547400-45549600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:45548000-45551600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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