Variant report

Variant	rs16849727
Chromosome Location	chr4:74460744-74460745
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10004505	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10009048	0.90[AMR][1000 genomes]
rs10011419	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10011536	1.00[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes]
rs10016403	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10019146	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10019320	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020054	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021827	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029673	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518115	0.81[CEU][hapmap]
rs10938078	0.81[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs10938079	0.86[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs10938088	0.91[AMR][1000 genomes]
rs11728915	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11729144	0.93[AMR][1000 genomes]
rs11733262	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs11943798	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1247593	0.84[EUR][1000 genomes]
rs1247651	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1247659	0.90[AMR][1000 genomes]
rs1247668	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247670	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs1247671	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12503916	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505842	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506668	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506675	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507775	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508661	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs13115877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13135124	0.90[AMR][1000 genomes]
rs13144296	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13149172	0.91[AMR][1000 genomes]
rs13353732	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1528915	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528916	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528917	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528918	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569204	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs1569207	0.90[AMR][1000 genomes]
rs1590115	0.85[EUR][1000 genomes]
rs1590116	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16849628	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849629	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849651	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849656	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849659	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849675	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849677	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17192413	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs1745300	0.83[MEX][hapmap]
rs1881611	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1919469	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1919479	0.83[EUR][1000 genomes]
rs1997332	0.86[CEU][hapmap]
rs2008288	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141470	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28407399	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450939	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28612539	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28693538	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28838047	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34123018	0.95[ASN][1000 genomes]
rs34773614	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34832471	0.84[EUR][1000 genomes]
rs34859660	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756073	0.81[EUR][1000 genomes]
rs4235119	0.90[CEU][hapmap]
rs4267703	0.86[CEU][hapmap]
rs4574378	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4618279	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62312137	0.93[AMR][1000 genomes]
rs6446937	0.83[MEX][hapmap];0.93[TSI][hapmap]
rs6446938	0.86[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs6837506	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852149	0.86[CEU][hapmap]
rs7665563	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665972	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667019	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667185	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674913	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676850	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676870	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676884	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682201	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687216	0.81[EUR][1000 genomes]
rs7695792	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695946	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696502	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997478	0.93[AMR][1000 genomes]
rs9997572	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9999939	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16849727	ART3	cis	cerebellum	SCAN
rs16849727	ANKRD17	cis	cerebellum	SCAN
rs16849727	CCNG2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74438000-74464800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:74440200-74472600	Weak transcription	Gastric	stomach
3	chr4:74441200-74464800	Weak transcription	Placenta	Placenta
4	chr4:74447600-74463400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:74449000-74470200	Weak transcription	Primary T cells from cord blood	blood
6	chr4:74449800-74461600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:74456400-74472200	Weak transcription	Colonic Mucosa	Colon
8	chr4:74456600-74464600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:74456800-74463400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:74456800-74463400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:74456800-74464600	Weak transcription	NHEK	skin
12	chr4:74457600-74464800	Weak transcription	Pancreas	Pancrea
13	chr4:74458000-74461800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:74458600-74464600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:74458800-74463600	Weak transcription	Fetal Intestine Large	intestine
16	chr4:74458800-74463600	Weak transcription	Thymus	Thymus
17	chr4:74459200-74464200	Weak transcription	Fetal Intestine Small	intestine
18	chr4:74459200-74464200	Weak transcription	HMEC	breast
19	chr4:74459400-74463400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:74460000-74461600	Weak transcription	GM12878-XiMat	blood
21	chr4:74460000-74462000	Genic enhancers	Fetal Thymus	thymus
22	chr4:74460200-74460800	Enhancers	Stomach Mucosa	stomach
23	chr4:74460400-74461800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:74460400-74463600	Weak transcription	Dnd41	blood
25	chr4:74460600-74461600	Weak transcription	A549	lung

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