Variant report

Variant	rs1498599
Chromosome Location	chr5:58355032-58355033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10037973	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10038704	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10043357	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045150	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10075067	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10075104	0.91[ASW][hapmap];0.86[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11958928	0.91[CEU][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11958956	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12652499	0.83[EUR][1000 genomes]
rs1363882	0.95[CEU][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1391650	0.95[CEU][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1391651	0.95[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1463817	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1498600	0.85[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409626	0.80[AMR][1000 genomes]
rs2910641	0.90[CHB][hapmap]
rs2910643	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2936190	0.81[CHB][hapmap]
rs2936193	0.81[CHB][hapmap]
rs5010782	0.94[CEU][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6867053	0.81[EUR][1000 genomes]
rs6898374	0.91[CEU][hapmap]
rs7730070	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1498599	NDUFAF2	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58336200-58375600	Weak transcription	Left Ventricle	heart
2	chr5:58336600-58358000	Weak transcription	Fetal Intestine Large	intestine
3	chr5:58336600-58358000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:58337400-58359000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:58338800-58359200	Weak transcription	Fetal Muscle Leg	muscle
6	chr5:58338800-58362000	Weak transcription	Gastric	stomach
7	chr5:58339000-58365200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:58340600-58359000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:58343600-58356400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:58346000-58359000	Weak transcription	Stomach Mucosa	stomach
11	chr5:58347200-58359200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:58348200-58362000	Weak transcription	Psoas Muscle	Psoas
13	chr5:58349600-58360600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:58350400-58360200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:58350600-58360200	Weak transcription	Fetal Stomach	stomach
16	chr5:58351000-58359000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:58351800-58357600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:58352000-58357000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:58352000-58357000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:58352400-58355800	Genic enhancers	A549	lung
21	chr5:58354800-58356600	Weak transcription	HepG2	liver
22	chr5:58354800-58357600	Strong transcription	Hela-S3	cervix
23	chr5:58355000-58355400	Enhancers	NHEK	skin

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