Variant report

Variant	rs13084377
Chromosome Location	chr3:156859189-156859190
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	chr3:156855375..156857018-chr3:156858174..156860003,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LEKR1-5	chr3:156857264-156860654	NONHSAT092888

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10440022	0.90[AMR][1000 genomes]
rs11917697	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12696046	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13060940	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13064954	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13076599	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13090731	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13091531	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13093524	0.90[AMR][1000 genomes]
rs13319093	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13321401	0.93[AMR][1000 genomes]
rs13324111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13326278	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28447380	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28513929	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28671546	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34154019	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34300533	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34508886	0.93[AMR][1000 genomes]
rs35196422	0.86[EUR][1000 genomes]
rs35295311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35988323	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3749215	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66686295	0.89[EUR][1000 genomes]
rs6764639	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71310497	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71310500	0.93[AMR][1000 genomes]
rs71310501	0.93[AMR][1000 genomes]
rs7613866	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9812766	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9814142	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814609	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9817693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821290	0.93[AMR][1000 genomes]
rs9827476	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9829650	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9830661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9856475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9856588	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9863805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9866141	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9868982	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[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	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156848400-156866000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:156848400-156866000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:156848600-156876600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:156849000-156860000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:156849000-156861000	Weak transcription	Dnd41	blood
6	chr3:156849000-156861800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:156849000-156862400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:156849200-156861600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:156849200-156861600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:156849400-156861600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:156849800-156864000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:156850000-156860200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:156850400-156860800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:156850400-156861600	Weak transcription	Hela-S3	cervix
15	chr3:156851000-156861000	Weak transcription	HUVEC	blood vessel
16	chr3:156852600-156873400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:156853200-156865400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:156853400-156872000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr3:156854000-156861200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:156854200-156860200	Weak transcription	Thymus	Thymus
21	chr3:156854800-156860200	Weak transcription	Esophagus	oesophagus
22	chr3:156855000-156860000	Weak transcription	Right Ventricle	heart
23	chr3:156855000-156860200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:156855000-156865800	Weak transcription	Aorta	Aorta
25	chr3:156855000-156866000	Weak transcription	Ovary	ovary
26	chr3:156855000-156872000	Weak transcription	Right Atrium	heart
27	chr3:156855200-156860000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:156855200-156860200	Weak transcription	Small Intestine	intestine
29	chr3:156855200-156861600	Weak transcription	Psoas Muscle	Psoas
30	chr3:156855200-156861800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:156855200-156862000	Weak transcription	Pancreas	Pancrea
32	chr3:156855200-156862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:156855400-156860000	Weak transcription	HSMM	muscle
34	chr3:156855400-156860200	Weak transcription	Spleen	Spleen
35	chr3:156855400-156860800	Weak transcription	GM12878-XiMat	blood
36	chr3:156855400-156862000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:156855400-156862200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:156855400-156862200	Weak transcription	HSMMtube	muscle
39	chr3:156855400-156865400	Weak transcription	Fetal Brain Male	brain
40	chr3:156855400-156865800	Weak transcription	Colonic Mucosa	Colon
41	chr3:156855400-156866000	Weak transcription	Fetal Heart	heart
42	chr3:156855400-156877000	Weak transcription	Gastric	stomach
43	chr3:156855600-156859200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:156855600-156859200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:156855600-156859200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:156855600-156859200	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:156855600-156860000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:156855600-156860000	Weak transcription	Brain Substantia Nigra	brain
49	chr3:156855600-156860200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:156855600-156860200	Weak transcription	Brain Anterior Caudate	brain

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