Variant report

Variant	rs344073
Chromosome Location	chr3:156547013-156547014
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	chr3:156390293..156396385-chr3:156542364..156548172,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10212230	0.84[JPT][hapmap]
rs10936040	0.83[JPT][hapmap]
rs10936043	0.83[JPT][hapmap]
rs11914959	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12634915	0.83[JPT][hapmap]
rs12638253	0.83[JPT][hapmap]
rs13070271	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13088978	0.84[JPT][hapmap]
rs1319418	0.94[CEU][hapmap]
rs1320011	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1384538	0.83[JPT][hapmap]
rs1574980	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1995425	0.84[JPT][hapmap]
rs2054880	0.83[JPT][hapmap]
rs2321290	0.83[JPT][hapmap]
rs2321291	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2321292	0.84[JPT][hapmap]
rs2321293	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2321455	0.84[JPT][hapmap]
rs2874488	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2874494	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2874495	0.84[JPT][hapmap]
rs343994	0.84[JPT][hapmap]
rs344079	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs344080	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs344082	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs344084	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344087	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs416600	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4234316	1.00[CEU][hapmap]
rs4315647	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs453219	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680311	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680312	0.84[JPT][hapmap]
rs4680313	0.85[EUR][1000 genomes]
rs4680314	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680317	0.84[JPT][hapmap]
rs6441101	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6762708	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6765353	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6780427	0.83[JPT][hapmap]
rs6783162	0.87[EUR][1000 genomes]
rs6784421	0.84[JPT][hapmap]
rs6803064	0.84[JPT][hapmap]
rs7615304	0.83[JPT][hapmap]
rs7622309	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7637701	0.84[JPT][hapmap]
rs7638330	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7638625	0.83[JPT][hapmap]
rs873337	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9826073	0.89[EUR][1000 genomes]
rs9837038	0.83[JPT][hapmap]
rs9844054	0.83[JPT][hapmap]
rs9847187	0.84[JPT][hapmap]
rs9862338	0.81[EUR][1000 genomes]
rs9863643	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9865905	0.84[JPT][hapmap]
rs9867621	0.82[JPT][hapmap]
rs9870137	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9871817	0.83[JPT][hapmap]
rs9876010	0.84[JPT][hapmap]
rs9876148	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs987724	0.83[JPT][hapmap]
rs9878585	0.84[JPT][hapmap]
rs9883439	1.00[CEU][hapmap];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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs344073	LINC00886	cis	Muscle Skeletal	GTEx
rs344073	LINC00886	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156545000-156559600	Weak transcription	Pancreas	Pancrea
2	chr3:156545200-156549800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:156545400-156551000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:156545600-156554000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:156545800-156558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:156546000-156549400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:156546000-156549800	Weak transcription	GM12878-XiMat	blood
8	chr3:156546400-156548000	Weak transcription	K562	blood
9	chr3:156547000-156550200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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