Variant report

Variant	rs62305056
Chromosome Location	chr4:100816226-100816227
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	POLR2A	chr4:100815167-100817274	K562	blood:	n/a	n/a
2	POLR2A	chr4:100815415-100816926	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:100815287-100816236	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:100815286-100816288	SK-N-SH	brain:	n/a	n/a
5	ZNF263	chr4:100814741-100816357	HEK293-T-REx	kidney:	n/a	chr4:100816100-100816109
6	POLR2A	chr4:100815312-100817046	GM12878	blood:	n/a	n/a
7	HCFC1	chr4:100814994-100816233	Hela-S3	cervix:	n/a	n/a
8	NRF1	chr4:100815497-100816357	SK-N-SH	brain:	n/a	chr4:100815756-100815767 chr4:100815756-100815767 chr4:100815753-100815767
9	MTA3	chr4:100815156-100816307	GM12878	blood:	n/a	n/a
10	REST	chr4:100814854-100816266	H1-neurons	neurons:	n/a	n/a
11	MXI1	chr4:100814691-100816419	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr4:100816213-100816339	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:100815145-100816513	GM19193	blood:	n/a	n/a
14	POLR2A	chr4:100814765-100817025	GM12891	blood:	n/a	n/a
15	STAT5A	chr4:100815178-100816288	GM12878	blood:	n/a	chr4:100815358-100815370 chr4:100815784-100815791
16	POLR2A	chr4:100815126-100816566	GM12878	blood:	n/a	n/a
17	POLR2A	chr4:100815238-100816513	Hela-S3	cervix:	n/a	n/a
18	PML	chr4:100815167-100816486	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:100813266..100817175-chr4:100865527..100871657,11	MCF-7	breast:
2	chr4:100814600..100817376-chr4:100869817..100872742,4	MCF-7	breast:
3	chr4:100815570..100818331-chr4:100848090..100849658,2	K562	blood:
4	chr4:100814213..100816552-chr4:100866797..100868818,3	MCF-7	breast:
5	chr4:100810623..100827791-chr4:100865444..100874425,55	K562	blood:
6	chr4:100799869..100822436-chr4:100866015..100873106,54	K562	blood:
7	chr4:100482462..100485382-chr4:100814090..100816679,3	MCF-7	breast:

Variant related genes	Relation type
LAMTOR3	TF binding region
ENSG00000164032	Chromatin interaction
ENSG00000164031	Chromatin interaction
ENSG00000145331	Chromatin interaction
ENSG00000138823	Chromatin interaction
ENSG00000245322	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10516459	0.98[EUR][1000 genomes]
rs12431	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs15924	0.93[EUR][1000 genomes]
rs17539582	0.93[EUR][1000 genomes]
rs17539883	0.93[EUR][1000 genomes]
rs17541426	0.98[EUR][1000 genomes]
rs17541690	0.85[EUR][1000 genomes]
rs17612178	0.81[EUR][1000 genomes]
rs17613746	0.93[EUR][1000 genomes]
rs17614270	0.81[EUR][1000 genomes]
rs2866181	0.81[EUR][1000 genomes]
rs41275723	0.95[EUR][1000 genomes]
rs62305039	0.81[EUR][1000 genomes]
rs62305041	0.90[EUR][1000 genomes]
rs62305044	0.81[EUR][1000 genomes]
rs62305046	0.95[EUR][1000 genomes]
rs62305049	0.83[EUR][1000 genomes]
rs62305052	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62305053	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62305055	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62305057	0.98[EUR][1000 genomes]
rs62305059	0.98[EUR][1000 genomes]
rs62306060	0.98[EUR][1000 genomes]
rs62306061	0.85[EUR][1000 genomes]
rs62306063	0.98[EUR][1000 genomes]
rs62306064	0.81[EUR][1000 genomes]
rs62306066	0.90[EUR][1000 genomes]
rs62306067	0.90[EUR][1000 genomes]
rs62306068	0.90[EUR][1000 genomes]
rs62306069	0.90[EUR][1000 genomes]
rs62306070	0.90[EUR][1000 genomes]
rs62306071	0.90[EUR][1000 genomes]
rs62306073	0.88[EUR][1000 genomes]
rs62306075	0.85[EUR][1000 genomes]
rs62306084	0.85[EUR][1000 genomes]
rs62306085	0.85[EUR][1000 genomes]
rs62306111	0.81[EUR][1000 genomes]
rs767652	0.93[EUR][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	nsv879661	chr4:100805207-100869635	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100813200-100816600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:100814400-100816400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr4:100814400-100816400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr4:100814400-100816400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr4:100814400-100816600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr4:100814600-100816400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr4:100814600-100816400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr4:100814600-100816400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:100814600-100816400	Active TSS	Psoas Muscle	Psoas
10	chr4:100814800-100816400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:100814800-100816400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:100814800-100816400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:100814800-100816600	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr4:100815000-100816400	Active TSS	Thymus	Thymus
15	chr4:100815000-100816600	Active TSS	Fetal Brain Female	brain
16	chr4:100815000-100816800	Active TSS	Fetal Lung	lung
17	chr4:100815200-100816400	Active TSS	Stomach Smooth Muscle	stomach
18	chr4:100815600-100816400	Active TSS	HepG2	liver
19	chr4:100815600-100816600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:100815600-100840000	Weak transcription	Small Intestine	intestine
21	chr4:100815800-100816400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr4:100815800-100816400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr4:100815800-100816400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:100815800-100816400	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr4:100815800-100816800	Flanking Active TSS	Dnd41	blood
26	chr4:100816000-100816400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:100816000-100816400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr4:100816000-100816400	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr4:100816000-100816400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:100816000-100816400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:100816000-100816400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:100816000-100816400	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr4:100816000-100816600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:100816000-100823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:100816000-100829600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr4:100816000-100839800	Weak transcription	Esophagus	oesophagus
37	chr4:100816000-100867000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:100816000-100867000	Weak transcription	Lung	lung
39	chr4:100816200-100816400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:100816200-100816400	Enhancers	Primary B cells from peripheral blood	blood
41	chr4:100816200-100816400	Enhancers	Primary T cells from cord blood	blood
42	chr4:100816200-100816400	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr4:100816200-100816400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr4:100816200-100816400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:100816200-100816400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:100816200-100816400	Weak transcription	Brain Germinal Matrix	brain
47	chr4:100816200-100816400	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:100816200-100816400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr4:100816200-100816400	Enhancers	Fetal Brain Male	brain
50	chr4:100816200-100816400	Enhancers	Fetal Intestine Large	intestine

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