Variant report

Variant	rs838606
Chromosome Location	chr3:143209571-143209572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143205251..143209634-chr3:143211909..143216344,4	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1097938	0.83[EUR][1000 genomes]
rs1097939	0.83[EUR][1000 genomes]
rs1097940	0.83[EUR][1000 genomes]
rs12486916	0.82[AFR][1000 genomes]
rs1525010	0.84[JPT][hapmap]
rs1525011	0.84[CHD][hapmap]
rs1530215	0.84[EUR][1000 genomes]
rs1530216	0.83[EUR][1000 genomes]
rs1660477	0.83[EUR][1000 genomes]
rs1660481	0.83[EUR][1000 genomes]
rs1723028	0.84[EUR][1000 genomes]
rs1723032	0.96[CEU][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1723034	0.86[CHD][hapmap]
rs1899217	0.82[AFR][1000 genomes]
rs2582353	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2582354	0.84[CHD][hapmap]
rs66599925	0.83[ASN][1000 genomes]
rs66925722	0.82[AFR][1000 genomes]
rs6780280	0.84[CHD][hapmap];0.80[JPT][hapmap]
rs6804097	0.84[CHD][hapmap]
rs716748	0.84[EUR][1000 genomes]
rs838605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs838607	0.94[ASN][1000 genomes]
rs838610	0.84[CHD][hapmap]
rs838612	0.84[CHD][hapmap]
rs838617	0.84[CHD][hapmap]
rs838621	0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs838624	0.96[CEU][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs838626	0.96[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs838629	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs838640	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs838641	0.87[ASN][1000 genomes]
rs838647	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs860800	0.85[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9289663	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs838606	PLOD2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143174400-143220400	Weak transcription	Fetal Lung	lung
2	chr3:143176800-143220400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:143179400-143220400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:143179800-143213400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:143185800-143213800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:143186000-143215600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:143186000-143223000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr3:143191200-143211000	Weak transcription	Primary T cells from cord blood	blood
9	chr3:143191400-143231000	Weak transcription	Primary B cells from cord blood	blood
10	chr3:143192400-143211400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr3:143192400-143215200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr3:143200200-143213800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:143201800-143226400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:143202200-143211800	Weak transcription	Esophagus	oesophagus
15	chr3:143204200-143212600	Weak transcription	Ovary	ovary
16	chr3:143209000-143214000	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:143209000-143226800	Weak transcription	Adipose Nuclei	Adipose

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