Variant report

Variant	rs2621312
Chromosome Location	chr3:159027205-159027206
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	chr3:159025201..159027938-chr3:159107782..159110251,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11707957	0.85[CEU][hapmap]
rs11715734	0.89[CEU][hapmap]
rs12635142	0.89[CEU][hapmap];0.82[CHB][hapmap]
rs13074822	0.87[CHB][hapmap]
rs1375403	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs1375405	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs1375407	0.96[CEU][hapmap];0.83[CHD][hapmap]
rs1448998	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[GIH][hapmap]
rs1449012	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs1449024	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs1449027	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1562671	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs1562672	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17795566	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1975601	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084507	0.87[CHB][hapmap]
rs2365478	0.87[CHB][hapmap]
rs2595232	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2595236	0.92[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];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2595243	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2595244	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs2595245	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2595246	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs2595247	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2595248	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2595250	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2595258	0.89[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap]
rs2621277	0.89[CEU][hapmap];0.82[CHB][hapmap];0.88[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	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2621292	0.89[CEU][hapmap];0.82[CHB][hapmap]
rs2621294	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2621295	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2621297	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs2621299	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2621300	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2621306	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2621310	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2621313	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2621314	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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35192832	0.94[ASN][1000 genomes]
rs3851358	0.89[CEU][hapmap];0.86[GIH][hapmap]
rs4645169	0.87[CHB][hapmap]
rs4680494	0.86[CHB][hapmap]
rs4680495	0.87[CHB][hapmap]
rs4680500	0.85[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap]
rs4680504	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs4680505	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs6441255	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs6782867	0.89[CEU][hapmap]
rs6787941	0.87[CHB][hapmap]
rs6790560	0.89[CEU][hapmap]
rs6807076	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap]
rs73166218	0.89[ASN][1000 genomes]
rs7428369	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs7634829	0.96[CEU][hapmap]
rs7646959	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap]
rs7649056	0.89[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2621312	ARPC2	trans	parietal	SCAN
rs2621312	MLF1	cis	cerebellum	SCAN
rs2621312	IQCJ	cis	parietal	SCAN
rs2621312	PTX3	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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