Variant report

Variant	rs10206953
Chromosome Location	chr2:55275612-55275613
allele	A/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	chr2:55274972-55276826	MCF10A-Er-Src	breast:	n/a	n/a
2	UBTF	chr2:55274752-55278735	K562	blood:	n/a	n/a
3	YY1	chr2:55275591-55276362	HepG2	liver:	n/a	chr2:55275988-55276000
4	CTCF	chr2:55275540-55275690	HAc	cerebellar:	n/a	n/a
5	CTCF	chr2:55275580-55275730	A549	lung:	n/a	n/a
6	MYC	chr2:55274782-55276825	MCF10A-Er-Src	breast:	n/a	chr2:55276654-55276661 chr2:55274921-55274929 chr2:55276651-55276662
7	POLR2A	chr2:55275602-55278945	HCT-116	colon:	n/a	n/a
8	CTCF	chr2:55275600-55275750	HA-sp	spinal cord:	n/a	n/a
9	TCF12	chr2:55275501-55278974	A549	lung:	n/a	chr2:55277949-55277956 chr2:55275946-55275954 chr2:55278509-55278518
10	MXI1	chr2:55275607-55278907	IMR90	lung:	n/a	n/a
11	MTA3	chr2:55275607-55276963	GM12878	blood:	n/a	n/a
12	CTCF	chr2:55275544-55275817	K562	blood:	n/a	n/a
13	TEAD4	chr2:55274780-55276604	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:55274825-55277952	HL-60	blood:	n/a	n/a
15	USF1	chr2:55275605-55276847	ECC-1	luminal epithelium:	n/a	chr2:55275804-55275815
16	JUN	chr2:55275513-55278923	K562	blood:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55277702-55277711 chr2:55278401-55278411
17	POLR2A	chr2:55275591-55278852	K562	blood:	n/a	n/a
18	MBD4	chr2:55275580-55276849	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:55275124-55278891	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr2:55274966-55278956	Hela-S3	cervix:	n/a	n/a
21	USF1	chr2:55275551-55276861	A549	lung:	n/a	chr2:55275804-55275815
22	MXI1	chr2:55274845-55276845	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr2:55275612-55275815	HepG2	liver:	n/a	n/a
24	CBX3	chr2:55275590-55276849	K562	blood:	n/a	n/a
25	MXI1	chr2:55274609-55279166	SK-N-SH	brain:	n/a	n/a
26	CHD1	chr2:55271552-55280181	IMR90	lung:	n/a	chr2:55276840-55276850
27	CTCF	chr2:55275560-55275710	HCM	heart:	n/a	n/a
28	USF1	chr2:55275545-55275994	ECC-1	luminal epithelium:	n/a	chr2:55275804-55275815
29	CTCF	chr2:55275560-55275710	GM12865	blood:	n/a	n/a
30	CTCF	chr2:55275586-55276934	K562	blood:	n/a	n/a
31	CTCF	chr2:55275600-55275750	AoAF	blood vessel:	n/a	n/a
32	SIN3AK20	chr2:55275599-55276962	MCF-7	breast:	n/a	n/a
33	MAX	chr2:55275572-55277020	ECC-1	luminal epithelium:	n/a	chr2:55276654-55276661 chr2:55276651-55276662 chr2:55276832-55276842
34	MAX	chr2:55275609-55276978	MCF-7	breast:	n/a	chr2:55276654-55276661 chr2:55276651-55276662 chr2:55276832-55276842
35	USF1	chr2:55275570-55276419	A549	lung:	n/a	chr2:55275804-55275815
36	PML	chr2:55275604-55278445	GM12878	blood:	n/a	n/a
37	MXI1	chr2:55275162-55276721	K562	blood:	n/a	n/a
38	TBL1XR1	chr2:55274565-55276771	K562	blood:	n/a	n/a
39	CTCF	chr2:55275580-55275730	HL-60	blood:	n/a	n/a
40	CTCF	chr2:55275600-55275750	NB4	blood:	n/a	n/a
41	RAD21	chr2:55275526-55276885	A549	lung:	n/a	n/a
42	MYBL2	chr2:55275593-55276851	HepG2	liver:	n/a	n/a
43	CHD1	chr2:55275134-55277601	H1-hESC	embryonic stem cell:	n/a	chr2:55276840-55276850
44	CTCF	chr2:55275600-55275750	Caco-2	colon:	n/a	n/a
45	MBD4	chr2:55275490-55276505	HepG2	liver:	n/a	n/a
46	MYC	chr2:55274905-55276926	NB4	blood:	n/a	chr2:55276654-55276661 chr2:55274921-55274929 chr2:55276651-55276662 chr2:55276832-55276842
47	CTCF	chr2:55275540-55275690	HVMF	connective:	n/a	n/a
48	TEAD4	chr2:55275585-55276533	ECC-1	luminal epithelium:	n/a	n/a
49	REST	chr2:55275594-55276813	K562	blood:	n/a	chr2:55276641-55276651 chr2:55276185-55276195
50	MYC	chr2:55275093-55276900	K562	blood:	n/a	chr2:55276654-55276661 chr2:55276651-55276662 chr2:55276832-55276842

No.	Distal block	Cell Line	Cell type
1	chr2:55241892..55242863-chr2:55275366..55276289,2	MCF-7	breast:
2	chr2:55274992..55277411-chr2:55494676..55497816,3	K562	blood:
3	chr2:55273795..55276620-chr2:55843969..55846667,2	K562	blood:
4	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
5	chr2:55240957..55243233-chr2:55273939..55276356,2	K562	blood:
6	chr2:55274992..55276773-chr2:55494676..55496447,2	K562	blood:
7	chr2:55275304..55279887-chr2:55458370..55461390,5	K562	blood:
8	chr2:55275046..55275830-chr2:55395421..55396072,2	MCF-7	breast:
9	chr2:54196421..54198197-chr2:55274517..55277399,2	MCF-7	breast:
10	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
11	chr2:55275101..55276800-chr2:55441099..55444085,2	K562	blood:
12	chr2:55274277..55275806-chr2:55323435..55326407,2	K562	blood:
13	chr2:55274620..55276240-chr2:55348004..55351084,3	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction
ENSG00000266376	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000200086	Chromatin interaction
ENSG00000203327	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000162994	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10170102	0.81[EUR][1000 genomes]
rs10175952	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10180207	0.80[EUR][1000 genomes]
rs10181115	0.81[EUR][1000 genomes]
rs10182203	0.86[EUR][1000 genomes]
rs10191748	0.84[AMR][1000 genomes]
rs10191774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10197533	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10207701	0.87[AMR][1000 genomes]
rs11125554	0.86[EUR][1000 genomes]
rs13387710	0.87[AMR][1000 genomes]
rs13400353	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13401780	0.98[EUR][1000 genomes]
rs13416852	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6545469	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545470	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6744637	0.98[EUR][1000 genomes]
rs6760773	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72912579	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7592869	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[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	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 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	chr2:55271400-55278200	Active TSS	HSMMtube	muscle
2	chr2:55272400-55279600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:55273000-55276200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:55273000-55276800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr2:55273200-55278400	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr2:55273200-55278400	Active TSS	GM12878-XiMat	blood
7	chr2:55273400-55276000	Weak transcription	Spleen	Spleen
8	chr2:55273400-55279800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr2:55273600-55276200	Active TSS	Right Atrium	heart
10	chr2:55273600-55276600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
11	chr2:55273800-55276200	Active TSS	Brain Germinal Matrix	brain
12	chr2:55273800-55278600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr2:55273800-55278600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:55273800-55279000	Active TSS	Psoas Muscle	Psoas
15	chr2:55273800-55279200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:55274000-55276200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr2:55274000-55278200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:55274000-55278200	Active TSS	NH-A	brain
19	chr2:55274200-55276200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:55274200-55276400	Active TSS	Fetal Brain Female	brain
21	chr2:55274200-55278400	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr2:55274200-55278600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:55274200-55278600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:55274200-55279000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:55274200-55279200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr2:55274200-55279600	Active TSS	HMEC	breast
27	chr2:55274400-55275800	Weak transcription	Small Intestine	intestine
28	chr2:55274400-55276000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:55274400-55278800	Active TSS	Fetal Brain Male	brain
30	chr2:55274600-55276000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:55274600-55276200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:55274600-55276200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:55274600-55276800	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr2:55274600-55276800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr2:55274600-55278000	Active TSS	Osteobl	bone
36	chr2:55274600-55278400	Active TSS	Fetal Muscle Leg	muscle
37	chr2:55274600-55278400	Active TSS	Fetal Stomach	stomach
38	chr2:55274600-55278600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:55274600-55278600	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr2:55274600-55278800	Active TSS	Aorta	Aorta
41	chr2:55274600-55278800	Active TSS	Fetal Muscle Trunk	muscle
42	chr2:55274600-55279200	Active TSS	NHEK	skin
43	chr2:55274800-55275800	Active TSS	Monocytes-CD14+_RO01746	blood
44	chr2:55274800-55276200	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr2:55274800-55278200	Active TSS	Fetal Intestine Large	intestine
46	chr2:55274800-55278400	Active TSS	Colon Smooth Muscle	Colon
47	chr2:55274800-55278400	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr2:55274800-55278600	Active TSS	Hela-S3	cervix
49	chr2:55274800-55278800	Active TSS	Ovary	ovary
50	chr2:55274800-55279000	Active TSS	H9 Cell Line	embryonic stem cell

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