Variant report

Variant	rs62242796
Chromosome Location	chr3:46029193-46029194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:46029138-46029417	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:46028886-46029623	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:46029057-46029419	HUVEC	blood vessel:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:45992659..45994641-chr3:46028942..46030792,2	K562	blood:
2	chr3:46021917..46024700-chr3:46027716..46030169,2	MCF-7	breast:
3	chr3:46024602..46026106-chr3:46028613..46030507,2	MCF-7	breast:
4	chr3:46008363..46011066-chr3:46026720..46029201,2	MCF-7	breast:
5	chr3:46028019..46029570-chr3:46035343..46037600,2	MCF-7	breast:
6	chr3:45986089..45986960-chr3:46029015..46029526,2	MCF-7	breast:
7	chr3:46026501..46029475-chr3:46032165..46035137,4	MCF-7	breast:

No data

Variant related genes	Relation type
FYCO1	TF binding region
ENSG00000172215	Chromatin interaction
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11130080	0.99[ASN][1000 genomes]
rs12495073	0.86[ASN][1000 genomes]
rs12630101	0.91[ASN][1000 genomes]
rs12635494	0.93[ASN][1000 genomes]
rs12635657	1.00[ASN][1000 genomes]
rs12639598	0.98[ASN][1000 genomes]
rs13060901	0.83[ASN][1000 genomes]
rs1392290	0.82[ASN][1000 genomes]
rs1392291	0.91[ASN][1000 genomes]
rs1500005	0.80[ASN][1000 genomes]
rs1601867	0.81[ASN][1000 genomes]
rs17078449	0.85[EUR][1000 genomes]
rs17078454	0.84[EUR][1000 genomes]
rs17078495	1.00[ASN][1000 genomes]
rs1994490	0.93[ASN][1000 genomes]
rs2054866	0.82[ASN][1000 genomes]
rs2234351	0.85[EUR][1000 genomes]
rs2234358	0.81[ASN][1000 genomes]
rs28808964	0.87[ASN][1000 genomes]
rs34381514	0.80[ASN][1000 genomes]
rs35465473	0.81[ASN][1000 genomes]
rs35537559	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733097	0.96[ASN][1000 genomes]
rs3733100	0.93[ASN][1000 genomes]
rs3774638	0.85[EUR][1000 genomes]
rs3774640	0.85[EUR][1000 genomes]
rs3796375	0.91[ASN][1000 genomes]
rs3796376	0.82[EUR][1000 genomes]
rs3821883	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821884	0.93[ASN][1000 genomes]
rs3851347	0.84[ASN][1000 genomes]
rs4234452	0.87[ASN][1000 genomes]
rs4333119	0.80[ASN][1000 genomes]
rs4683156	0.82[ASN][1000 genomes]
rs4683157	0.80[ASN][1000 genomes]
rs57204020	0.85[EUR][1000 genomes]
rs59226168	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59767267	0.85[EUR][1000 genomes]
rs60237998	0.83[EUR][1000 genomes]
rs60539039	0.89[ASN][1000 genomes]
rs60779624	0.85[EUR][1000 genomes]
rs62242787	0.85[EUR][1000 genomes]
rs62245108	0.84[EUR][1000 genomes]
rs67044455	1.00[ASN][1000 genomes]
rs6764042	0.83[ASN][1000 genomes]
rs6778225	0.84[EUR][1000 genomes]
rs6778324	0.85[EUR][1000 genomes]
rs6778896	1.00[ASN][1000 genomes]
rs6781668	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6800954	0.83[EUR][1000 genomes]
rs6805094	0.83[ASN][1000 genomes]
rs730983	1.00[ASN][1000 genomes]
rs737452	1.00[ASN][1000 genomes]
rs751552	0.93[ASN][1000 genomes]
rs751553	0.93[ASN][1000 genomes]
rs7616464	0.80[ASN][1000 genomes]
rs7623460	0.83[ASN][1000 genomes]
rs7631809	0.84[EUR][1000 genomes]
rs931704	1.00[ASN][1000 genomes]
rs936939	0.85[EUR][1000 genomes]
rs9849015	0.81[ASN][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46000000-46029600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:46010200-46029600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:46010200-46033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:46013600-46034000	Genic enhancers	Fetal Thymus	thymus
5	chr3:46019400-46030000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:46020000-46034200	Genic enhancers	Dnd41	blood
7	chr3:46021400-46036200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:46021600-46034000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:46023000-46029800	Strong transcription	Primary T cells from cord blood	blood
10	chr3:46025000-46029400	Genic enhancers	Fetal Intestine Small	intestine
11	chr3:46025000-46031600	Weak transcription	Fetal Kidney	kidney
12	chr3:46025200-46031800	Enhancers	Right Atrium	heart
13	chr3:46025600-46032400	Enhancers	Stomach Mucosa	stomach
14	chr3:46025600-46033000	Enhancers	Right Ventricle	heart
15	chr3:46025800-46031200	Enhancers	HSMMtube	muscle
16	chr3:46026000-46031800	Enhancers	NHDF-Ad	bronchial
17	chr3:46026200-46029800	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr3:46026200-46031800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:46026200-46032000	Enhancers	Ovary	ovary
20	chr3:46026200-46032000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr3:46026200-46032000	Enhancers	NHLF	lung
22	chr3:46026400-46029200	Enhancers	Adipose Nuclei	Adipose
23	chr3:46026400-46029400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:46026400-46029400	Enhancers	Fetal Lung	lung
25	chr3:46026400-46031400	Enhancers	HSMM	muscle
26	chr3:46026400-46031600	Enhancers	Fetal Intestine Large	intestine
27	chr3:46026400-46031800	Enhancers	Fetal Muscle Leg	muscle
28	chr3:46026400-46033800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:46026400-46034600	Genic enhancers	Primary T cells fromperipheralblood	blood
30	chr3:46026600-46029200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:46026600-46029400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:46026600-46029600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:46026600-46029800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:46026600-46030000	Enhancers	Colonic Mucosa	Colon
35	chr3:46026600-46031400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:46026600-46031400	Enhancers	Lung	lung
37	chr3:46026600-46031600	Enhancers	Pancreas	Pancrea
38	chr3:46026600-46031800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:46026600-46032200	Enhancers	Liver	Liver
40	chr3:46026600-46032200	Enhancers	Duodenum Mucosa	Duodenum
41	chr3:46026600-46033000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:46026600-46033000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:46026600-46033000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:46026600-46036200	Enhancers	Left Ventricle	heart
45	chr3:46026800-46029200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:46026800-46029800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:46026800-46032800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:46026800-46033400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:46026800-46033600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:46026800-46033800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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