Variant report

Variant	rs13084945
Chromosome Location	chr3:99976779-99976780
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	POLR2A	chr3:99976317-99976904	U87	brain:	n/a	n/a
2	RCOR1	chr3:99976302-99977089	IMR90	lung:	n/a	n/a
3	FOXP2	chr3:99976394-99976805	SK-N-MC	brain:	n/a	n/a
4	RCOR1	chr3:99976531-99976869	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:99973186..99975181-chr3:99976513..99979207,3	K562	blood:
2	chr3:99971442..99977426-chr3:99977772..99982553,8	MCF-7	breast:
3	chr3:99974835..99977676-chr3:100052303..100055041,2	MCF-7	breast:

Variant related genes	Relation type
TBC1D23	TF binding region
ENSG00000114021	Chromatin interaction
ENSG00000036054	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13074029	1.00[AFR][1000 genomes]
rs13096852	0.84[EUR][1000 genomes]
rs13098066	0.84[EUR][1000 genomes]
rs34745071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71620020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99964600-99978600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:99964800-99979000	Weak transcription	Aorta	Aorta
3	chr3:99965200-99978800	Weak transcription	NH-A	brain
4	chr3:99965600-99978800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:99966600-99979000	Weak transcription	Gastric	stomach
6	chr3:99968000-99978800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:99973000-99978800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:99973400-99978400	Weak transcription	Fetal Stomach	stomach
9	chr3:99973400-99978800	Weak transcription	Brain Substantia Nigra	brain
10	chr3:99973400-99978800	Weak transcription	Fetal Intestine Large	intestine
11	chr3:99973400-99979000	Weak transcription	Fetal Intestine Small	intestine
12	chr3:99973400-99979000	Weak transcription	Left Ventricle	heart
13	chr3:99973400-99979000	Weak transcription	HSMM	muscle
14	chr3:99973600-99978200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:99973600-99978800	Weak transcription	HSMMtube	muscle
16	chr3:99973800-99978800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:99974000-99978400	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:99974200-99977000	Enhancers	HepG2	liver
19	chr3:99975200-99977000	Enhancers	Adipose Nuclei	Adipose
20	chr3:99975200-99977200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:99975400-99976800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:99975400-99976800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:99975400-99976800	Enhancers	NHLF	lung
24	chr3:99975400-99977000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:99975400-99977200	Enhancers	Osteobl	bone
26	chr3:99975600-99978600	Weak transcription	Fetal Lung	lung
27	chr3:99975800-99976800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:99976000-99976800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:99976000-99976800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:99976000-99977600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:99976200-99976800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:99976200-99976800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr3:99976200-99976800	Enhancers	Ovary	ovary
34	chr3:99976200-99976800	Enhancers	Right Atrium	heart
35	chr3:99976200-99976800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:99976200-99977000	Enhancers	Fetal Muscle Leg	muscle
37	chr3:99976200-99977000	Enhancers	K562	blood
38	chr3:99976200-99977000	Flanking Active TSS	NHDF-Ad	bronchial
39	chr3:99976400-99978800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:99976600-99976800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:99976600-99976800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:99976600-99976800	Enhancers	Esophagus	oesophagus
43	chr3:99976600-99976800	Enhancers	Fetal Muscle Trunk	muscle
44	chr3:99976600-99976800	Enhancers	Lung	lung
45	chr3:99976600-99976800	Enhancers	Pancreas	Pancrea
46	chr3:99976600-99977000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:99976600-99977200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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