Variant report

Variant	rs59902026
Chromosome Location	chr3:112358927-112358928
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:112358726-112360545	SK-N-SH	brain:	n/a	n/a
2	MAX	chr3:112358802-112360786	SK-N-SH	brain:	n/a	chr3:112360464-112360473
3	CEBPB	chr3:112358594-112360673	A549	lung:	n/a	chr3:112358750-112358761
4	MAFK	chr3:112358924-112360416	Hela-S3	cervix:	n/a	chr3:112359917-112359932
5	GATA3	chr3:112358736-112360473	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:112358884-112362166	IMR90	lung:	n/a	n/a
7	POLR2A	chr3:112358922-112360408	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr3:112358601-112359392	A549	lung:	n/a	chr3:112358750-112358761
9	PBX3	chr3:112358816-112359563	SK-N-SH	brain:	n/a	n/a
10	CEBPB	chr3:112358564-112359476	IMR90	lung:	n/a	chr3:112358750-112358761
11	FOSL2	chr3:112358894-112360538	A549	lung:	n/a	n/a
12	TCF7L2	chr3:112358910-112359718	Hela-S3	cervix:	n/a	chr3:112359141-112359155 chr3:112359143-112359152 chr3:112359140-112359156 chr3:112359140-112359156
13	TCF12	chr3:112358661-112360765	SK-N-SH	brain:	n/a	n/a
14	EP300	chr3:112358782-112359095	SK-N-SH_RA	brain:	n/a	chr3:112358991-112359000
15	POLR2A	chr3:112358851-112360352	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr3:112358908-112360532	HUVEC	blood vessel:	n/a	n/a
17	GATA3	chr3:112358828-112360501	A549	lung:	n/a	n/a
18	FOSL2	chr3:112358917-112360366	SK-N-SH	brain:	n/a	n/a
19	BCL3	chr3:112358844-112360481	A549	lung:	n/a	n/a
20	EP300	chr3:112358819-112359377	SK-N-SH_RA	brain:	n/a	chr3:112358991-112359000
21	RAD21	chr3:112358892-112359725	IMR90	lung:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:112326392..112328017-chr3:112358236..112359844,2	MCF-7	breast:
2	chr3:112358576..112361067-chr3:112520655..112523598,3	MCF-7	breast:
3	chr3:112289268..112293035-chr3:112358216..112361029,3	MCF-7	breast:
4	chr3:112358478..112360877-chr3:112708365..112711089,3	MCF-7	breast:
5	chr3:112358855..112360949-chr3:112737036..112738900,2	K562	blood:
6	chr3:112354638..112357493-chr3:112357624..112362114,5	K562	blood:
7	chr3:112358680..112360592-chr3:112737016..112739347,2	MCF-7	breast:
8	chr3:112357856..112364091-chr3:112692717..112699765,9	MCF-7	breast:
9	chr3:112278745..112284115-chr3:112357887..112361363,11	MCF-7	breast:
10	chr3:112358506..112363260-chr3:112706755..112711649,8	K562	blood:
11	chr3:112279172..112282504-chr3:112358640..112361542,6	MCF-7	breast:
12	chr3:112358697..112360499-chr3:112735766..112739410,3	MCF-7	breast:
13	chr3:112279230..112282432-chr3:112358112..112361671,5	K562	blood:
14	chr3:112358089..112359762-chr3:112460166..112463073,2	MCF-7	breast:
15	chr3:112357488..112363507-chr3:112707947..112711649,7	K562	blood:
16	chr3:112279230..112281440-chr3:112358030..112362501,6	K562	blood:
17	chr3:112358718..112361602-chr3:112709202..112711684,5	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC80	TF binding region
ENSG00000163607	Chromatin interaction
ENSG00000163608	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000240057	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000242770	Chromatin interaction
ENSG00000163606	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16859905	0.83[AFR][1000 genomes]
rs28364604	0.85[AFR][1000 genomes]
rs60584468	0.83[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112342600-112359600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:112345200-112359400	Weak transcription	Esophagus	oesophagus
3	chr3:112354000-112359000	Flanking Active TSS	NH-A	brain
4	chr3:112354000-112359200	Weak transcription	Fetal Brain Female	brain
5	chr3:112354000-112360600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:112354400-112359000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:112354600-112359400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:112354800-112359000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:112354800-112359000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:112354800-112359000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:112354800-112360000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr3:112355000-112359000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:112355400-112359600	Active TSS	Colonic Mucosa	Colon
14	chr3:112355800-112360200	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr3:112356000-112360600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr3:112356200-112359000	Weak transcription	Brain Anterior Caudate	brain
17	chr3:112356200-112360000	Active TSS	Brain Substantia Nigra	brain
18	chr3:112357000-112359000	Weak transcription	Aorta	Aorta
19	chr3:112357200-112359200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:112357200-112360400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:112357200-112361000	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr3:112358000-112359000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr3:112358000-112359200	Enhancers	Pancreas	Pancrea
24	chr3:112358000-112360400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:112358000-112360400	Active TSS	Right Ventricle	heart
26	chr3:112358200-112359000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:112358200-112359000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:112358200-112359400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:112358400-112359200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:112358400-112359200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr3:112358400-112359200	Enhancers	Fetal Heart	heart
32	chr3:112358400-112359600	Active TSS	Rectal Smooth Muscle	rectum
33	chr3:112358400-112360400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:112358600-112359000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:112358600-112359000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:112358600-112359000	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr3:112358600-112359200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:112358600-112359200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
39	chr3:112358600-112359200	Flanking Active TSS	Fetal Kidney	kidney
40	chr3:112358600-112359200	Flanking Active TSS	Hela-S3	cervix
41	chr3:112358600-112359400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:112358600-112359400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr3:112358600-112359400	Weak transcription	Left Ventricle	heart
44	chr3:112358600-112360000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:112358600-112360000	Active TSS	Fetal Intestine Large	intestine
46	chr3:112358600-112360000	Active TSS	Placenta Amnion	Placenta Amnion
47	chr3:112358600-112360000	Active TSS	HSMMtube	muscle
48	chr3:112358600-112360200	Active TSS	Brain Hippocampus Middle	brain
49	chr3:112358600-112360200	Active TSS	Colon Smooth Muscle	Colon
50	chr3:112358600-112360400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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