Variant report

Variant	rs13073116
Chromosome Location	chr3:112051693-112051694
allele	G/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	NFIC	chr3:112051494-112052894	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:112051646-112053318	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:112051517-112053276	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr3:112051512-112053366	H1-neurons	neurons:	n/a	n/a
5	IKZF1	chr3:112051645-112051950	GM12878	blood:	n/a	n/a
6	MTA3	chr3:112051621-112053371	GM12878	blood:	n/a	n/a
7	RUNX3	chr3:112051647-112053029	GM12878	blood:	n/a	n/a
8	MAZ	chr3:112051673-112052196	GM12878	blood:	n/a	chr3:112051951-112051961
9	REST	chr3:112051640-112053368	H1-neurons	neurons:	n/a	chr3:112052555-112052568
10	CHD1	chr3:112051578-112053376	H1-hESC	embryonic stem cell:	n/a	chr3:112052032-112052042 chr3:112051984-112051994 chr3:112051953-112051963
11	FOXM1	chr3:112051638-112052284	GM12878	blood:	n/a	n/a
12	PML	chr3:112051584-112053213	GM12878	blood:	n/a	chr3:112052233-112052241
13	REST	chr3:112051331-112054778	H1-neurons	neurons:	n/a	chr3:112052555-112052568
14	E2F6	chr3:112051658-112052776	H1-hESC	embryonic stem cell:	n/a	chr3:112052497-112052508 chr3:112052494-112052511 chr3:112052497-112052508 chr3:112052494-112052511
15	ZNF384	chr3:112051530-112052023	GM12878	blood:	n/a	n/a
16	TAF1	chr3:112051631-112053361	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
CD200	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11714917	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11716857	1.00[ASN][1000 genomes]
rs17513726	0.83[ASN][1000 genomes]
rs2280462	0.91[ASN][1000 genomes]
rs2399411	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4234416	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4550804	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56037521	0.83[ASN][1000 genomes]
rs62264134	0.83[ASN][1000 genomes]
rs62264135	0.83[ASN][1000 genomes]
rs62264136	0.83[ASN][1000 genomes]
rs62264137	0.83[ASN][1000 genomes]
rs6438066	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6438067	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438068	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6771014	1.00[ASN][1000 genomes]
rs6774405	0.91[ASN][1000 genomes]
rs6809034	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7619941	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs939576	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs939577	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs939578	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9814088	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9818526	0.88[AFR][1000 genomes];1.00[ASN][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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112050600-112054200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr3:112050800-112051800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:112050800-112054200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr3:112051000-112053600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr3:112051000-112053800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:112051000-112054000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:112051000-112054200	Active TSS	Placenta	Placenta
8	chr3:112051200-112051800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:112051400-112051800	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr3:112051400-112051800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:112051400-112052000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr3:112051400-112052000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:112051400-112053400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:112051400-112053600	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:112051400-112053600	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr3:112051400-112053600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr3:112051400-112054200	Active TSS	Fetal Brain Female	brain
18	chr3:112051400-112054200	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr3:112051400-112054400	Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr3:112051400-112054400	Active TSS	GM12878-XiMat	blood
21	chr3:112051400-112054600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:112051600-112051800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:112051600-112051800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:112051600-112051800	Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr3:112051600-112051800	Bivalent/Poised TSS	Primary T cells fromperipheralblood	blood
26	chr3:112051600-112051800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:112051600-112051800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:112051600-112051800	Bivalent/Poised TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:112051600-112051800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr3:112051600-112051800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
31	chr3:112051600-112051800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:112051600-112051800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:112051600-112051800	Active TSS	Duodenum Mucosa	Duodenum
34	chr3:112051600-112051800	Enhancers	Esophagus	oesophagus
35	chr3:112051600-112051800	Active TSS	Fetal Muscle Trunk	muscle
36	chr3:112051600-112051800	Active TSS	Fetal Muscle Leg	muscle
37	chr3:112051600-112051800	Enhancers	Left Ventricle	heart
38	chr3:112051600-112051800	Active TSS	Right Atrium	heart
39	chr3:112051600-112051800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr3:112051600-112051800	Bivalent/Poised TSS	A549	lung
41	chr3:112051600-112051800	Active TSS	HMEC	breast
42	chr3:112051600-112051800	Bivalent Enhancer	NHEK	skin
43	chr3:112051600-112052000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:112051600-112052000	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr3:112051600-112052000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr3:112051600-112052000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr3:112051600-112052000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:112051600-112052000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:112051600-112052000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
50	chr3:112051600-112052000	Active TSS	Fetal Stomach	stomach

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