Variant report

Variant	rs16889129
Chromosome Location	chr5:58349882-58349883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10061553	0.80[ASN][1000 genomes]
rs1006431	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11738454	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13181587	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498604	0.88[EUR][1000 genomes]
rs1498605	0.91[EUR][1000 genomes]
rs1498606	0.84[ASW][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968009	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs4699934	0.89[EUR][1000 genomes]
rs4700319	0.81[CEU][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs6450500	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16889129	MIER3	cis	cerebellum	SCAN
rs16889129	DDX4	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58336200-58375600	Weak transcription	Left Ventricle	heart
2	chr5:58336600-58351800	Weak transcription	Fetal Intestine Small	intestine
3	chr5:58336600-58358000	Weak transcription	Fetal Intestine Large	intestine
4	chr5:58336600-58358000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:58337400-58359000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:58338400-58350200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:58338800-58351800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:58338800-58359200	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:58338800-58362000	Weak transcription	Gastric	stomach
10	chr5:58339000-58351600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:58339000-58365200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:58340600-58359000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr5:58343600-58356400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:58346000-58359000	Weak transcription	Stomach Mucosa	stomach
15	chr5:58347200-58353000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:58347200-58359200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr5:58348200-58351200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:58348200-58362000	Weak transcription	Psoas Muscle	Psoas
19	chr5:58348400-58350000	Weak transcription	Hela-S3	cervix
20	chr5:58348400-58352200	Weak transcription	Right Ventricle	heart
21	chr5:58348400-58354200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:58348600-58351200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:58349600-58360600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:58349800-58350000	Flanking Active TSS	A549	lung

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