Variant report

Variant	rs2621314
Chromosome Location	chr3:159030345-159030346
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158998052..159000120-chr3:159030298..159031893,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11707957	0.89[CEU][hapmap]
rs11715734	0.92[CEU][hapmap]
rs12635142	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs13074822	0.87[CHB][hapmap]
rs1375403	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs1375405	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs1375407	0.92[CEU][hapmap];0.86[CHD][hapmap]
rs1448998	0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[GIH][hapmap]
rs1449012	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs1449024	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs1449027	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1562671	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs1562672	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17795566	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1975601	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084507	0.87[CHB][hapmap]
rs2365478	0.87[CHB][hapmap]
rs2595232	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2595236	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2595238	0.92[ASN][1000 genomes]
rs2595239	0.90[ASN][1000 genomes]
rs2595242	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2595243	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2595244	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[YRI][hapmap]
rs2595245	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2595246	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs2595247	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2595248	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2595250	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2595253	1.00[YRI][hapmap]
rs2595258	0.82[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap]
rs2621277	0.83[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap]
rs2621280	0.83[EUR][1000 genomes]
rs2621282	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2621284	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2621290	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2621292	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs2621294	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2621295	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2621297	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs2621299	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2621300	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2621306	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2621310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2621312	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs2621313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35192832	0.94[ASN][1000 genomes]
rs3851358	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs4645169	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs4680494	0.86[CHB][hapmap]
rs4680495	0.87[CHB][hapmap]
rs4680500	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap]
rs4680504	0.89[CEU][hapmap];0.81[GIH][hapmap]
rs4680505	0.89[CEU][hapmap];0.86[GIH][hapmap]
rs6441255	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs6782867	0.92[CEU][hapmap]
rs6787941	0.87[CHB][hapmap]
rs6790560	0.92[CEU][hapmap]
rs6807076	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap]
rs73166218	0.89[ASN][1000 genomes]
rs7428369	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs7634829	0.92[CEU][hapmap]
rs7646959	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap]
rs7649056	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs9879667	0.82[CHB][hapmap]

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	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2621314	ARPC2	trans	parietal	SCAN
rs2621314	PTX3	cis	parietal	SCAN
rs2621314	IQCJ	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159030000-159030800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:159030000-159031200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:159030200-159030600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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