Variant report

Variant	rs2233209
Chromosome Location	chr5:52406006-52406007
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	TCF12	chr5:52405135-52406035	A549	lung:	n/a	n/a
2	POLR2A	chr5:52405204-52406024	GM12878	blood:	n/a	n/a
3	E2F6	chr5:52405260-52406043	A549	lung:	n/a	chr5:52405598-52405607 chr5:52405594-52405601 chr5:52405466-52405477 chr5:52405475-52405487 chr5:52405621-52405630
4	POLR2A	chr5:52405275-52406034	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr5:52405022-52406119	K562	blood:	n/a	n/a
6	POLR2A	chr5:52405156-52406077	U87	brain:	n/a	n/a
7	POLR2A	chr5:52404973-52406398	HepG2	liver:	n/a	n/a
8	TAF1	chr5:52405398-52406053	MCF-7	breast:	n/a	n/a
9	POLR2A	chr5:52405345-52406038	HL-60	blood:	n/a	n/a
10	MAX	chr5:52405231-52406052	ECC-1	luminal epithelium:	n/a	chr5:52405647-52405657
11	SIN3AK20	chr5:52405312-52406076	MCF-7	breast:	n/a	n/a
12	POLR2A	chr5:52405293-52406304	PBDE	blood:	n/a	n/a
13	POLR2A	chr5:52405192-52406039	GM12878	blood:	n/a	n/a
14	MYBL2	chr5:52405380-52406020	HepG2	liver:	n/a	n/a
15	PAX5	chr5:52405241-52406071	GM12878	blood:	n/a	n/a
16	MAX	chr5:52405215-52406083	HepG2	liver:	n/a	chr5:52405647-52405657
17	POLR2A	chr5:52405387-52406039	H1-neurons	neurons:	n/a	n/a
18	EGR1	chr5:52405042-52406019	HCT-116	colon:	n/a	chr5:52405648-52405658 chr5:52405598-52405607
19	POLR2A	chr5:52405264-52406050	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr5:52404965-52406408	K562	blood:	n/a	n/a
21	POLR2A	chr5:52405218-52406090	A549	lung:	n/a	n/a
22	MAX	chr5:52404852-52406021	SK-N-SH	brain:	n/a	chr5:52405647-52405657
23	MBD4	chr5:52405549-52406024	HepG2	liver:	n/a	n/a
24	MYC	chr5:52405262-52406236	K562	blood:	n/a	chr5:52405647-52405657
25	TFAP2C	chr5:52405151-52406265	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr5:52405190-52406085	MCF-7	breast:	n/a	n/a
27	MYC	chr5:52405032-52406040	K562	blood:	n/a	chr5:52405647-52405657
28	POLR2A	chr5:52405119-52406120	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr5:52405079-52406119	PFSK-1	brain:	n/a	n/a
30	MAX	chr5:52404802-52406149	A549	lung:	n/a	chr5:52405647-52405657
31	MXI1	chr5:52404860-52406050	GM12878	blood:	n/a	n/a
32	SMARCB1	chr5:52405293-52406013	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr5:52405206-52406071	GM12892	blood:	n/a	n/a
34	MAX	chr5:52404843-52406064	ECC-1	luminal epithelium:	n/a	chr5:52405647-52405657
35	NRF1	chr5:52405073-52406077	SK-N-SH	brain:	n/a	chr5:52405596-52405607 chr5:52405597-52405611 chr5:52405620-52405631 chr5:52405597-52405608 chr5:52405649-52405658 chr5:52405667-52405678 chr5:52405650-52405661
36	POLR2A	chr5:52405203-52406041	Gliobla	brain:	n/a	n/a
37	MAX	chr5:52405290-52406014	SK-N-SH	brain:	n/a	chr5:52405647-52405657
38	REST	chr5:52404904-52406190	H1-neurons	neurons:	n/a	n/a
39	MXI1	chr5:52404860-52406008	Hela-S3	cervix:	n/a	n/a
40	REST	chr5:52405283-52406029	A549	lung:	n/a	n/a
41	MTA3	chr5:52405064-52406066	GM12878	blood:	n/a	n/a
42	POLR2A	chr5:52405181-52406060	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr5:52405168-52406136	SK-N-MC	brain:	n/a	n/a
44	MAX	chr5:52405177-52406255	K562	blood:	n/a	chr5:52405647-52405657
45	POLR2A	chr5:52405189-52406040	PFSK-1	brain:	n/a	n/a
46	MAX	chr5:52404817-52406185	Hela-S3	cervix:	n/a	chr5:52405647-52405657
47	POLR2A	chr5:52405030-52406236	NB4	blood:	n/a	n/a
48	PML	chr5:52405340-52406027	K562	blood:	n/a	n/a
49	POLR2A	chr5:52405235-52406036	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr5:52405194-52406007	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:52384729..52387843-chr5:52404184..52407459,4	MCF-7	breast:
2	chr17:58469116..58469940-chr5:52405166..52406062,2	MCF-7	breast:
3	chr5:52282064..52285632-chr5:52404082..52406997,3	MCF-7	breast:

Variant related genes	Relation type
MOCS2	TF binding region
ENSG00000170832	Chromatin interaction
ENSG00000272123	Chromatin interaction
ENSG00000141371	Chromatin interaction
ENSG00000164171	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12515434	0.82[EUR][1000 genomes]
rs16880875	1.00[EUR][1000 genomes]
rs2910977	0.83[EUR][1000 genomes]
rs3212517	0.83[EUR][1000 genomes]
rs3212519	0.83[EUR][1000 genomes]
rs3212578	0.83[EUR][1000 genomes]
rs3212623	0.86[EUR][1000 genomes]
rs3212632	0.98[EUR][1000 genomes]
rs62359375	0.95[EUR][1000 genomes]
rs62359376	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv442948	chr5:52404519-52409439	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52403800-52406600	Active TSS	K562	blood
2	chr5:52404000-52406200	Active TSS	NHLF	lung
3	chr5:52404400-52406400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:52404400-52406400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr5:52404400-52406400	Active TSS	Psoas Muscle	Psoas
6	chr5:52404400-52406400	Active TSS	GM12878-XiMat	blood
7	chr5:52404600-52406200	Active TSS	Brain Hippocampus Middle	brain
8	chr5:52404600-52406200	Active TSS	Colon Smooth Muscle	Colon
9	chr5:52404600-52406200	Active TSS	Fetal Intestine Large	intestine
10	chr5:52404600-52406400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:52404600-52406400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr5:52404600-52406400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:52404600-52406400	Active TSS	Brain Anterior Caudate	brain
14	chr5:52404600-52406600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:52404600-52406600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:52404600-52406600	Active TSS	A549	lung
17	chr5:52404600-52406600	Active TSS	HepG2	liver
18	chr5:52404600-52406600	Active TSS	NHDF-Ad	bronchial
19	chr5:52404600-52407000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr5:52404800-52406200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr5:52404800-52406200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr5:52404800-52406200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr5:52404800-52406200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:52404800-52406200	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr5:52404800-52406200	Active TSS	Aorta	Aorta
26	chr5:52404800-52406200	Active TSS	Esophagus	oesophagus
27	chr5:52404800-52406200	Active TSS	Fetal Kidney	kidney
28	chr5:52404800-52406200	Active TSS	Fetal Thymus	thymus
29	chr5:52404800-52406200	Active TSS	Rectal Smooth Muscle	rectum
30	chr5:52404800-52406400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr5:52404800-52406400	Active TSS	H9 Cell Line	embryonic stem cell
32	chr5:52404800-52406400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:52404800-52406400	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr5:52404800-52406400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:52404800-52406400	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr5:52404800-52406400	Active TSS	Left Ventricle	heart
37	chr5:52404800-52406400	Active TSS	Ovary	ovary
38	chr5:52404800-52406400	Active TSS	Right Atrium	heart
39	chr5:52404800-52406400	Active TSS	Right Ventricle	heart
40	chr5:52404800-52406600	Active TSS	H1 Cell Line	embryonic stem cell
41	chr5:52404800-52406600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:52404800-52406600	Active TSS	Fetal Intestine Small	intestine
43	chr5:52404800-52406800	Active TSS	Pancreas	Pancrea
44	chr5:52405000-52406200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr5:52405000-52406200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:52405000-52406200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr5:52405000-52406200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:52405000-52406200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:52405000-52406200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr5:52405000-52406200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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