Variant report

Variant	rs3909374
Chromosome Location	chr19:42133048-42133049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1001062	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1001578	0.89[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs10520341	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11083633	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11083635	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11671944	0.90[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11672173	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11672853	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11673394	0.89[ASW][hapmap]
rs11880469	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11880615	0.90[EUR][1000 genomes]
rs11880655	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12462395	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12979028	0.91[EUR][1000 genomes]
rs34652740	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4347734	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4803492	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8182595	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8182615	0.89[EUR][1000 genomes]
rs8182619	0.89[EUR][1000 genomes]
rs917552	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057624	chr19:42057334-42152828	Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1058847	chr19:42057334-42172442	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1063241	chr19:42057334-42175160	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv519408	chr19:42066279-42171906	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3319146	chr19:42082639-42212929	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv3319147	chr19:42082742-42212770	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3422975	chr19:42106166-42212774	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3909374	PLEKHA4	cis	parietal	SCAN
rs3909374	ATF5	cis	parietal	SCAN
rs3909374	GIPR	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42130400-42133600	Active TSS	Primary B cells from cord blood	blood
2	chr19:42131800-42133200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr19:42132000-42133200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr19:42132000-42133800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
5	chr19:42132400-42134200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:42132600-42133800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr19:42132600-42136800	Weak transcription	Spleen	Spleen
8	chr19:42132800-42133200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
9	chr19:42132800-42133600	Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr19:42132800-42133800	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr19:42132800-42134000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:42133000-42133400	Bivalent/Poised TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:42133000-42133400	Bivalent/Poised TSS	Adipose Nuclei	Adipose
14	chr19:42133000-42133400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
15	chr19:42133000-42133400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
16	chr19:42133000-42133400	Active TSS	Rectal Mucosa Donor 29	rectum

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