Variant report

Variant	rs2202152
Chromosome Location	chr1:45506964-45506965
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45503364..45509535-chr1:45510898..45517046,6	K562	blood:
2	chr1:45505490..45509535-chr1:45509540..45512957,3	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11211074	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1144868	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1226747	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1612575	0.91[CHD][hapmap]
rs1938301	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2088956	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2105458	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2228084	1.00[CHD][hapmap]
rs2356302	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs238249	0.91[CHD][hapmap]
rs2997461	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2997465	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs3009969	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs3009974	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3009979	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs34134455	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs346684	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs346693	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs346696	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs346697	0.83[AMR][1000 genomes]
rs346698	0.83[AMR][1000 genomes]
rs346700	0.83[AMR][1000 genomes]
rs346703	0.91[CHD][hapmap]
rs346706	0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs346707	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap]
rs346708	0.83[AMR][1000 genomes]
rs346717	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs346719	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs346724	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs346725	0.91[CHD][hapmap]
rs346732	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs346733	0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs346735	0.81[AMR][1000 genomes]
rs346736	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs365108	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs3738246	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3850855	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3850856	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs454624	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs4660834	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660839	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4660841	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs4660842	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6429557	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6664113	0.86[ASN][1000 genomes]
rs6688318	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6702327	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7528534	0.90[CHD][hapmap];0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2202152	NSUN4	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45480800-45510400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:45481200-45510200	Weak transcription	Lung	lung
3	chr1:45481200-45525000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:45481200-45527400	Weak transcription	Left Ventricle	heart
5	chr1:45482000-45523800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:45491800-45516400	Weak transcription	Spleen	Spleen
7	chr1:45492000-45507600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:45497400-45525400	Weak transcription	Gastric	stomach
9	chr1:45498000-45525600	Weak transcription	Pancreas	Pancrea
10	chr1:45499200-45516200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:45500400-45516600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:45501400-45516600	Weak transcription	Small Intestine	intestine
13	chr1:45501800-45508000	Weak transcription	Brain Substantia Nigra	brain
14	chr1:45501800-45516200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:45501800-45521200	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:45501800-45527000	Weak transcription	Fetal Brain Male	brain
17	chr1:45502000-45507600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:45502000-45507600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:45502000-45508000	Weak transcription	Brain Angular Gyrus	brain
20	chr1:45502000-45508000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:45502000-45508000	Weak transcription	Fetal Brain Female	brain
22	chr1:45502000-45508200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:45502000-45508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:45502000-45510600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:45502000-45512800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:45502000-45523800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:45502400-45507800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:45502400-45523000	Weak transcription	Aorta	Aorta
29	chr1:45503400-45508200	Weak transcription	Brain Anterior Caudate	brain
30	chr1:45504000-45509800	Strong transcription	Brain Germinal Matrix	brain
31	chr1:45504000-45510400	Weak transcription	Hela-S3	cervix
32	chr1:45504200-45524200	Weak transcription	Esophagus	oesophagus
33	chr1:45504400-45524000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:45504600-45508400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:45504800-45508000	Weak transcription	Ovary	ovary
36	chr1:45504800-45516400	Weak transcription	Fetal Intestine Large	intestine
37	chr1:45505000-45526000	Weak transcription	Fetal Stomach	stomach
38	chr1:45505200-45508400	Weak transcription	HepG2	liver
39	chr1:45505200-45508600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:45505200-45508800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:45505200-45514600	Weak transcription	Fetal Intestine Small	intestine
42	chr1:45505800-45508000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:45506200-45508400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:45506600-45508000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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