Variant report

Variant	rs4957640
Chromosome Location	chr5:111601600-111601601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13158768	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13160791	0.84[EUR][1000 genomes]
rs13166322	0.82[EUR][1000 genomes]
rs13183224	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13184442	1.00[CEU][hapmap];0.92[GIH][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17134318	0.88[EUR][1000 genomes]
rs17134331	0.84[EUR][1000 genomes]
rs17134343	0.85[GIH][hapmap];0.84[EUR][1000 genomes]
rs17134350	0.86[EUR][1000 genomes]
rs34069146	0.84[EUR][1000 genomes]
rs34136685	0.86[EUR][1000 genomes]
rs34489497	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34947473	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35182061	0.84[EUR][1000 genomes]
rs35212577	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35368594	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35538937	0.86[EUR][1000 genomes]
rs35625614	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35705963	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35808967	0.84[EUR][1000 genomes]
rs35843631	0.86[EUR][1000 genomes]
rs35938930	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4485968	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4957643	0.84[EUR][1000 genomes]
rs4958023	1.00[CEU][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4958026	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4958033	0.86[EUR][1000 genomes]
rs62364081	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62364135	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62364136	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62364138	0.89[EUR][1000 genomes]
rs62364140	0.86[EUR][1000 genomes]
rs62364141	0.86[EUR][1000 genomes]
rs62364144	0.82[EUR][1000 genomes]
rs62364145	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62365192	0.84[EUR][1000 genomes]
rs62370377	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6865000	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7714295	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
6	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4957640	PRDX2	trans	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111564600-111609600	Weak transcription	Pancreas	Pancrea
2	chr5:111567400-111602400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:111568600-111609600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:111584800-111605600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:111585800-111606000	Weak transcription	Spleen	Spleen
6	chr5:111586600-111626400	Weak transcription	Gastric	stomach
7	chr5:111590400-111609600	Weak transcription	Psoas Muscle	Psoas
8	chr5:111590400-111628200	Weak transcription	Aorta	Aorta
9	chr5:111590600-111605800	Weak transcription	Right Ventricle	heart
10	chr5:111590800-111617000	Weak transcription	Left Ventricle	heart
11	chr5:111590800-111617200	Weak transcription	Esophagus	oesophagus
12	chr5:111590800-111618200	Weak transcription	Right Atrium	heart
13	chr5:111591400-111606600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:111593400-111605600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:111594000-111606200	Weak transcription	HUVEC	blood vessel
16	chr5:111594000-111611600	Weak transcription	Placenta	Placenta
17	chr5:111594800-111605800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:111594800-111615000	Weak transcription	Fetal Kidney	kidney
19	chr5:111595400-111604600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:111596000-111605800	Weak transcription	Hela-S3	cervix
21	chr5:111596200-111603400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:111598600-111606200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:111599000-111603200	Weak transcription	Adipose Nuclei	Adipose
24	chr5:111599400-111602200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:111599800-111603400	Enhancers	Fetal Heart	heart
26	chr5:111600800-111612800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:111601000-111602200	Weak transcription	Lung	lung
28	chr5:111601400-111601600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:111601600-111601800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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