Variant report

Variant	rs4253332
Chromosome Location	chr4:187179803-187179804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs34899763	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4253273	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4253283	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4253294	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4253313	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4861709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs925453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv530178	chr4:186659940-187478310	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv931977	chr4:186912987-187364756	Active TSS Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv869299	chr4:186958290-187192748	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1033203	chr4:186990348-187333476	Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv537431	chr4:186990348-187333476	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv461864	chr4:187006806-187257004	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv596392	chr4:187006806-187257004	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv461865	chr4:187072383-187366649	Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv596401	chr4:187072383-187366649	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv1022059	chr4:187082701-187183953	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv881472	chr4:187152142-187187005	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv3330372	chr4:187179493-187180035	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4253332	ODZ3	cis	parietal	SCAN
rs4253332	CYP4V2	cis	multi-tissue	Pritchard
rs4253332	KLKB1	cis	cerebellum	SCAN
rs4253332	F11	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187131800-187181600	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:187149800-187181600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr4:187149800-187186800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:187150200-187187200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:187151000-187187200	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:187154000-187182000	Weak transcription	Primary T cells from cord blood	blood
7	chr4:187158400-187181400	Weak transcription	Fetal Intestine Large	intestine
8	chr4:187170000-187180200	Weak transcription	Brain Angular Gyrus	brain
9	chr4:187170800-187182000	Weak transcription	Right Ventricle	heart
10	chr4:187171200-187182000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:187171400-187182000	Weak transcription	Spleen	Spleen
12	chr4:187171600-187182000	Weak transcription	Gastric	stomach
13	chr4:187171800-187181000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:187172000-187182000	Weak transcription	Adipose Nuclei	Adipose
15	chr4:187172200-187182000	Weak transcription	Esophagus	oesophagus
16	chr4:187173400-187180200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:187173600-187181200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:187173600-187181600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:187173600-187181600	Weak transcription	Psoas Muscle	Psoas
20	chr4:187173600-187182000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:187173600-187182000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:187173800-187181000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:187173800-187182000	Weak transcription	Left Ventricle	heart
24	chr4:187175400-187180200	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr4:187177400-187180400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:187177400-187191800	Weak transcription	Right Atrium	heart
27	chr4:187178400-187180200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:187178800-187180000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:187178800-187180400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:187179000-187180000	Strong transcription	Brain Anterior Caudate	brain
31	chr4:187179000-187181400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr4:187179200-187180000	ZNF genes & repeats	Lung	lung
33	chr4:187179200-187180400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:187179400-187180200	Enhancers	Pancreas	Pancrea
35	chr4:187179400-187180200	Enhancers	HepG2	liver
36	chr4:187179600-187180200	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:187179600-187181200	Weak transcription	Fetal Intestine Small	intestine
38	chr4:187179800-187180200	Flanking Active TSS	Liver	Liver
39	chr4:187179800-187181400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:187179800-187182000	Weak transcription	Brain Cingulate Gyrus	brain

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