Variant report

Variant	rs73852854
Chromosome Location	chr3:111388552-111388553
allele	A/G
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	CTCF	chr3:111388540-111388690	GM12865	blood:	n/a	n/a
2	CTCF	chr3:111387607-111388565	SK-N-SH	brain:	n/a	chr3:111387949-111387962 chr3:111387946-111387964 chr3:111387947-111387963 chr3:111387948-111387969
3	GATA3	chr3:111388371-111389537	SK-N-SH	brain:	n/a	chr3:111389372-111389379
4	RAD21	chr3:111387484-111388709	SK-N-SH	brain:	n/a	chr3:111387947-111387966
5	CTCF	chr3:111388540-111388690	GM12872	blood:	n/a	n/a
6	CTCF	chr3:111387323-111389525	A549	lung:	n/a	chr3:111387949-111387962 chr3:111387946-111387964 chr3:111387947-111387963 chr3:111387948-111387969
7	TCF12	chr3:111388380-111389440	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111388505..111391497-chr3:111391977..111394861,5	MCF-7	breast:

Variant related genes	Relation type
PLCXD2	TF binding region
ENSG00000240891	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs6437999	0.81[AMR][1000 genomes]
rs73852858	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7639515	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111384400-111389200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:111384400-111389400	Enhancers	NHEK	skin
3	chr3:111384400-111389600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:111384600-111389400	Enhancers	HMEC	breast
5	chr3:111384800-111388800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:111384800-111390000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:111385000-111392600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:111385200-111388600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:111385400-111392600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:111385800-111388600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr3:111386400-111390400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:111386600-111388800	Enhancers	Hela-S3	cervix
13	chr3:111386600-111389600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:111386800-111388600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:111386800-111388600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr3:111386800-111388600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:111386800-111388600	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr3:111386800-111389400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:111386800-111389400	Enhancers	A549	lung
20	chr3:111386800-111389800	Enhancers	Osteobl	bone
21	chr3:111386800-111392400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:111387000-111388600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr3:111387000-111392400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:111387000-111392600	Enhancers	Primary T cells from cord blood	blood
25	chr3:111387000-111392600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:111387000-111392600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:111387800-111388600	Enhancers	Fetal Intestine Large	intestine
28	chr3:111387800-111388800	Enhancers	NH-A	brain
29	chr3:111387800-111392600	Weak transcription	GM12878-XiMat	blood
30	chr3:111388000-111388600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:111388000-111388600	Enhancers	Fetal Intestine Small	intestine
32	chr3:111388000-111389200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:111388000-111389200	Enhancers	HSMMtube	muscle
34	chr3:111388000-111389400	Enhancers	HSMM	muscle
35	chr3:111388000-111389800	Enhancers	Placenta	Placenta
36	chr3:111388000-111390000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:111388000-111390200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:111388000-111391600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:111388000-111392000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:111388000-111392200	Weak transcription	Thymus	Thymus
41	chr3:111388000-111392400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:111388200-111388600	Enhancers	HepG2	liver
43	chr3:111388200-111389800	Weak transcription	Dnd41	blood
44	chr3:111388200-111390000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:111388200-111391000	Weak transcription	Primary B cells from cord blood	blood
46	chr3:111388200-111391000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:111388200-111391400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:111388200-111391800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:111388200-111391800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:111388200-111392200	Weak transcription	Primary B cells from peripheral blood	blood

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