Variant report

Variant	rs838640
Chromosome Location	chr3:143200689-143200690
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	chr3:143193715..143198774-chr3:143199748..143204167,7	K562	blood:
2	chr3:143196850..143198555-chr3:143200057..143202935,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10212321	0.94[ASN][1000 genomes]
rs10212557	0.94[ASN][1000 genomes]
rs1097938	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1097939	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1097940	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12490020	0.92[ASN][1000 genomes]
rs1525010	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1525011	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1530215	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1530216	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1660477	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1660481	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16853629	0.94[ASN][1000 genomes]
rs1723028	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1723031	0.95[ASN][1000 genomes]
rs1723032	0.84[CEU][hapmap]
rs1723034	0.86[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs1852059	0.94[ASN][1000 genomes]
rs1978912	0.95[ASN][1000 genomes]
rs2582353	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2582354	0.82[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs57914974	0.94[ASN][1000 genomes]
rs60765365	0.94[ASN][1000 genomes]
rs66508148	0.94[ASN][1000 genomes]
rs66599925	0.99[ASN][1000 genomes]
rs6768834	0.94[ASN][1000 genomes]
rs6779984	0.94[ASN][1000 genomes]
rs6780280	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6793614	0.94[ASN][1000 genomes]
rs6802358	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs6804097	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs716748	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs838605	0.85[ASN][1000 genomes]
rs838606	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]
rs838609	0.95[ASN][1000 genomes]
rs838610	0.82[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs838611	0.95[ASN][1000 genomes]
rs838612	0.82[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs838614	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs838615	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs838617	0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs838619	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs838621	0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs838624	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs838625	0.91[ASN][1000 genomes]
rs838626	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs838629	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs838641	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs838647	0.95[CEU][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs860800	0.82[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs865709	0.95[ASN][1000 genomes]
rs9289663	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][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
rs838640	PLOD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143159600-143200800	Weak transcription	Esophagus	oesophagus
2	chr3:143163800-143203400	Weak transcription	Ovary	ovary
3	chr3:143174400-143220400	Weak transcription	Fetal Lung	lung
4	chr3:143176800-143220400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:143177200-143200800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:143177800-143204400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:143178000-143203200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:143179400-143220400	Weak transcription	Brain Substantia Nigra	brain
9	chr3:143179800-143213400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:143185800-143213800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:143186000-143201200	Weak transcription	Adipose Nuclei	Adipose
12	chr3:143186000-143215600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:143186000-143223000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:143186400-143204400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:143191200-143211000	Weak transcription	Primary T cells from cord blood	blood
16	chr3:143191400-143231000	Weak transcription	Primary B cells from cord blood	blood
17	chr3:143192400-143211400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr3:143192400-143215200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr3:143196600-143203800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:143197000-143202800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:143197400-143201200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:143197400-143201600	Weak transcription	Fetal Stomach	stomach
23	chr3:143197400-143203800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:143197800-143202200	Enhancers	HSMM	muscle
25	chr3:143198600-143201600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:143198600-143202200	Enhancers	NHDF-Ad	bronchial
27	chr3:143199400-143201200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr3:143199600-143200800	Weak transcription	HSMMtube	muscle
29	chr3:143199600-143201000	Weak transcription	Dnd41	blood
30	chr3:143199600-143202200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr3:143199600-143203800	Weak transcription	NH-A	brain
32	chr3:143199800-143200800	Weak transcription	Colonic Mucosa	Colon
33	chr3:143199800-143200800	Weak transcription	Stomach Mucosa	stomach
34	chr3:143199800-143200800	Weak transcription	Osteobl	bone
35	chr3:143199800-143201200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:143199800-143202200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:143199800-143203600	Weak transcription	A549	lung
38	chr3:143199800-143205200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:143200200-143213800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:143200600-143200800	Enhancers	Aorta	Aorta

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