Variant report

Variant	rs3774640
Chromosome Location	chr3:45983479-45983480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr3:45983478-45984603	SH-SY5Y	brain:	n/a	chr3:45983942-45983950
2	POLR2A	chr3:45983005-45983876	K562	blood:	n/a	n/a
3	POLR2A	chr3:45983370-45983593	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45978904..45980774-chr3:45983050..45984937,2	MCF-7	breast:

Variant related genes	Relation type
CXCR6	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs13066048	0.81[ASN][1000 genomes]
rs17078449	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17078454	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234351	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35537559	0.85[EUR][1000 genomes]
rs3774638	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774639	0.81[ASN][1000 genomes]
rs3796376	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821883	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4683153	0.95[ASN][1000 genomes]
rs4683154	0.81[ASN][1000 genomes]
rs57204020	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59226168	0.83[EUR][1000 genomes]
rs59767267	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60237998	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60779624	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62242787	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62242788	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62242796	0.85[EUR][1000 genomes]
rs62245106	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62245108	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6778225	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6778324	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6781121	0.95[ASN][1000 genomes]
rs6781668	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6800954	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7631809	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs936939	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
2	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:45963200-45985200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:45970200-45988200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:45972800-45988600	Weak transcription	Small Intestine	intestine
6	chr3:45973400-45986400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:45973800-45988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:45973800-45991400	Weak transcription	Brain Germinal Matrix	brain
9	chr3:45974400-45988000	Weak transcription	Fetal Kidney	kidney
10	chr3:45977400-45987000	Weak transcription	Fetal Lung	lung
11	chr3:45977400-45988000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:45977600-45987600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:45978000-45988000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:45978200-45988200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:45978400-45983800	Weak transcription	Spleen	Spleen
16	chr3:45978400-45986600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:45978800-45994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:45979000-45987200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:45979000-45988200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:45979000-45993000	Weak transcription	Stomach Mucosa	stomach
21	chr3:45979200-45987200	Weak transcription	Colonic Mucosa	Colon
22	chr3:45979200-45987800	Weak transcription	Brain Anterior Caudate	brain
23	chr3:45979200-45987800	Weak transcription	HepG2	liver
24	chr3:45979200-45988200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:45979600-45984200	Weak transcription	Liver	Liver
26	chr3:45979800-45983600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:45979800-45983600	Weak transcription	Gastric	stomach
28	chr3:45980200-45984800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
29	chr3:45980400-45984800	Enhancers	Placenta	Placenta
30	chr3:45980600-45984000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:45980800-45983600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:45980800-45983600	Weak transcription	Adipose Nuclei	Adipose
33	chr3:45980800-45983800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:45980800-45984400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr3:45980800-45986800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr3:45980800-45988000	Weak transcription	NH-A	brain
37	chr3:45980800-45989200	Weak transcription	Fetal Brain Male	brain
38	chr3:45980800-46013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:45981000-45983600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:45981000-45983800	Weak transcription	Right Atrium	heart
41	chr3:45981000-45986400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:45981000-45986600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:45981000-45986600	Weak transcription	Brain Angular Gyrus	brain
44	chr3:45981000-45987800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:45981000-45988000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:45981000-45988000	Weak transcription	NHDF-Ad	bronchial
47	chr3:45981000-45988000	Weak transcription	Osteobl	bone
48	chr3:45981000-45988200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:45981000-45990400	Weak transcription	Fetal Brain Female	brain
50	chr3:45981000-45993400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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