Variant report

Variant	rs62279927
Chromosome Location	chr3:161089263-161089264
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:27)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160282107..160285570-chr3:161087865..161089951,3	MCF-7	breast:
2	chr3:161038392..161046344-chr3:161085640..161093564,25	MCF-7	breast:
3	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
4	chr20:31169325..31171437-chr3:161088010..161089511,2	MCF-7	breast:
5	chr22:31475291..31477772-chr3:161087457..161089639,2	MCF-7	breast:
6	chr13:37572263..37575251-chr3:161088174..161090196,2	MCF-7	breast:
7	chr20:45982415..45984680-chr3:161089076..161091449,2	MCF-7	breast:
8	chr3:136470318..136472005-chr3:161088059..161090755,2	MCF-7	breast:
9	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
10	chr17:58040687..58043660-chr3:161087957..161089475,2	MCF-7	breast:
11	chr2:97535160..97536953-chr3:161088031..161090726,2	MCF-7	breast:
12	chr3:161088166..161091113-chr7:44082932..44085823,2	MCF-7	breast:
13	chr17:57181517..57184200-chr3:161086879..161089854,2	MCF-7	breast:
14	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:
15	chr3:161087384..161090083-chr9:131900097..131902606,2	MCF-7	breast:
16	chr3:160472518..160475131-chr3:161089184..161091851,3	MCF-7	breast:
17	chr22:30683032..30685513-chr3:161089094..161092006,2	MCF-7	breast:
18	chr14:73955822..73958124-chr3:161089151..161090979,2	MCF-7	breast:
19	chr16:89786488..89788334-chr3:161087418..161089454,2	MCF-7	breast:
20	chr20:49346270..49349571-chr3:161087854..161090885,3	MCF-7	breast:
21	chr3:161088340..161091318-chr9:131938931..131941651,2	MCF-7	breast:
22	chr1:149858017..149860169-chr3:161088036..161090033,2	MCF-7	breast:
23	chr16:83986674..83988846-chr3:161086778..161089338,2	MCF-7	breast:
24	chr3:160587600..160589495-chr3:161088974..161091016,2	MCF-7	breast:
25	chr3:161087820..161090854-chr7:26238154..26241381,3	MCF-7	breast:
26	chr12:12713891..12716367-chr3:161087265..161090021,2	MCF-7	breast:
27	chr3:161088194..161090248-chr9:137216086..137218582,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B3GALNT1-3	chr3:161089223-161089305	NONHSAT093015

No data

Variant related genes	Relation type
ENSG00000186350	Chromatin interaction
ENSG00000204055	Chromatin interaction
ENSG00000255242	Chromatin interaction
ENSG00000240138	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000170468	Chromatin interaction
ENSG00000140961	Chromatin interaction
ENSG00000075399	Chromatin interaction
ENSG00000158805	Chromatin interaction
ENSG00000122565	Chromatin interaction
ENSG00000183963	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000239282	Chromatin interaction
ENSG00000260572	Chromatin interaction
ENSG00000189050	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000188483	Chromatin interaction
ENSG00000118007	Chromatin interaction
ENSG00000119383	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000122566	Chromatin interaction
ENSG00000136279	Chromatin interaction
ENSG00000186432	Chromatin interaction
ENSG00000111266	Chromatin interaction
ENSG00000120699	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000163590	Chromatin interaction
ENSG00000120697	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000228156	Chromatin interaction
ENSG00000261758	Chromatin interaction
ENSG00000224738	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000267302	Chromatin interaction
ENSG00000184270	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs16832063	1.00[EUR][1000 genomes]
rs16832129	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16832137	0.82[EUR][1000 genomes]
rs16847274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278032	0.89[AMR][1000 genomes]
rs62278054	0.89[AMR][1000 genomes]
rs62278056	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62279886	0.85[EUR][1000 genomes]
rs62279918	1.00[EUR][1000 genomes]
rs62279920	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62279922	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62279923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62279924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62279925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62279929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62279930	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62279931	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62279948	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62279949	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62279950	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62279954	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62279955	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73162552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73162554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73162598	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]

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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers 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	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161088000-161091400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:161088400-161089800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:161088400-161091000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr3:161088600-161089400	Bivalent Enhancer	Fetal Lung	lung
5	chr3:161088600-161090600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr3:161088600-161090600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr3:161088600-161090800	Active TSS	Stomach Mucosa	stomach
8	chr3:161089000-161089400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:161089000-161089400	Active TSS	NHEK	skin
10	chr3:161089000-161089600	Flanking Active TSS	Fetal Brain Female	brain
11	chr3:161089000-161090200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:161089000-161090400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr3:161089000-161090600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr3:161089000-161090600	Active TSS	Brain Anterior Caudate	brain
15	chr3:161089000-161090600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr3:161089000-161090600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:161089000-161090800	Active TSS	Brain Germinal Matrix	brain
18	chr3:161089000-161091000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:161089000-161091000	Active TSS	Brain Cingulate Gyrus	brain
20	chr3:161089200-161089400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
21	chr3:161089200-161089400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
22	chr3:161089200-161089400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
23	chr3:161089200-161089400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
24	chr3:161089200-161089400	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:161089200-161089400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr3:161089200-161089400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:161089200-161089400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:161089200-161089400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:161089200-161089400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:161089200-161089400	Bivalent Enhancer	Adipose Nuclei	Adipose
31	chr3:161089200-161089400	Bivalent/Poised TSS	Colonic Mucosa	Colon
32	chr3:161089200-161089400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
33	chr3:161089200-161089400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr3:161089200-161089400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
35	chr3:161089200-161089400	Bivalent Enhancer	Placenta	Placenta
36	chr3:161089200-161089400	Bivalent Enhancer	Fetal Thymus	thymus
37	chr3:161089200-161089400	Flanking Bivalent TSS/Enh	Left Ventricle	heart
38	chr3:161089200-161089400	Enhancers	Pancreas	Pancrea
39	chr3:161089200-161089400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
40	chr3:161089200-161089400	Flanking Active TSS	Right Ventricle	heart
41	chr3:161089200-161089400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
42	chr3:161089200-161089400	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr3:161089200-161089400	Bivalent Enhancer	HUVEC	blood vessel
44	chr3:161089200-161089400	Flanking Bivalent TSS/Enh	NH-A	brain
45	chr3:161089200-161089600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:161089200-161089600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:161089200-161089600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:161089200-161089600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:161089200-161089600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr3:161089200-161089600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--

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