Variant report

Variant	rs62264749
Chromosome Location	chr3:119747919-119747920
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	chr3:119745451..119747987-chr3:119811711..119814390,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1I2-3	chr3:119747587-119748715	NONHSAT091415

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10433404	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934500	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10934502	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934503	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934505	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934506	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934507	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915717	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12054090	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12108149	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629015	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12630829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632325	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12634476	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12634889	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12635018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638973	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1574154	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16830567	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1870931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980718	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28831519	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3814057	0.82[ASN][1000 genomes]
rs3814058	0.82[ASN][1000 genomes]
rs4340737	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4624596	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4688042	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4688046	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688047	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688053	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688054	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688059	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56728675	0.81[ASN][1000 genomes]
rs57939147	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs58493895	0.81[ASN][1000 genomes]
rs58863896	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60235167	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60393216	0.81[ASN][1000 genomes]
rs62264706	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62264708	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62264714	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62264734	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62264739	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264742	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264743	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264747	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62266274	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62266277	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62266281	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6773751	0.80[AFR][1000 genomes]
rs6797459	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6808874	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7633279	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7639388	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119731400-119752400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:119732600-119748400	Weak transcription	Brain Angular Gyrus	brain
3	chr3:119732600-119748600	Weak transcription	HSMM	muscle
4	chr3:119732600-119757800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:119732800-119749200	Weak transcription	Fetal Stomach	stomach
6	chr3:119734800-119750000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:119735000-119751600	Weak transcription	Primary B cells from cord blood	blood
8	chr3:119737000-119749400	Weak transcription	Stomach Mucosa	stomach
9	chr3:119737000-119751800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr3:119737400-119751800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:119737400-119754000	Weak transcription	Small Intestine	intestine
12	chr3:119737800-119757200	Weak transcription	A549	lung
13	chr3:119739400-119756000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:119739600-119749400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:119740000-119758200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:119740600-119748400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:119740800-119753400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:119741000-119758000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:119741200-119748400	Weak transcription	HSMMtube	muscle
20	chr3:119741200-119758400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:119741600-119749000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:119741800-119753600	Weak transcription	Thymus	Thymus
23	chr3:119742000-119748400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:119742000-119754400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:119742000-119758000	Weak transcription	NHDF-Ad	bronchial
26	chr3:119742600-119752200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:119742600-119757000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:119744200-119748400	Weak transcription	Spleen	Spleen
29	chr3:119744200-119758000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:119744400-119758400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:119744800-119751600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:119744800-119753600	Weak transcription	Fetal Thymus	thymus
33	chr3:119744800-119758000	Weak transcription	NHEK	skin
34	chr3:119745000-119748000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:119745000-119750200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:119745000-119751800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:119745000-119757000	Weak transcription	Dnd41	blood
38	chr3:119745200-119748400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:119745200-119750200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:119745200-119758400	Weak transcription	HepG2	liver
41	chr3:119745400-119748400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:119745400-119751800	Weak transcription	Primary T cells from cord blood	blood
43	chr3:119745400-119758400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:119746200-119749400	Enhancers	Brain Hippocampus Middle	brain
45	chr3:119746400-119748400	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:119747000-119748600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:119747000-119748600	Enhancers	Brain Cingulate Gyrus	brain
48	chr3:119747000-119748800	Enhancers	Brain Substantia Nigra	brain
49	chr3:119747000-119749000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr3:119747000-119750400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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