Variant report

Variant	rs2252544
Chromosome Location	chr13:48878292-48878293
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	POLR2A	chr13:48877201-48878314	K562	blood:	n/a	n/a
2	MAX	chr13:48877186-48878981	NB4	blood:	n/a	chr13:48878320-48878330
3	REST	chr13:48877064-48878501	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr13:48877438-48878358	A549	lung:	n/a	n/a
5	POLR2A	chr13:48876826-48878925	Raji	blood:	n/a	n/a
6	CTCF	chr13:48878251-48878316	MCF-7	breast:	n/a	chr13:48878298-48878311 chr13:48878295-48878308
7	E2F6	chr13:48878154-48878374	K562	blood:	n/a	n/a
8	MXI1	chr13:48877097-48879046	IMR90	lung:	n/a	n/a
9	POLR2A	chr13:48877279-48878963	GM12892	blood:	n/a	n/a
10	CTCF	chr13:48878180-48878330	AG04449	skin:	n/a	chr13:48878298-48878311 chr13:48878295-48878308
11	BHLHE40	chr13:48877484-48879186	GM12878	blood:	n/a	n/a
12	MAZ	chr13:48877260-48879409	GM12878	blood:	n/a	chr13:48878320-48878330
13	POLR2A	chr13:48877280-48878401	Gliobla	brain:	n/a	n/a
14	POLR2A	chr13:48877094-48879260	Hela-S3	cervix:	n/a	n/a
15	TAF1	chr13:48877568-48878317	HepG2	liver:	n/a	n/a
16	E2F6	chr13:48878102-48878340	K562	blood:	n/a	n/a
17	POLR2A	chr13:48877114-48878403	HL-60	blood:	n/a	n/a
18	POLR2A	chr13:48877127-48878391	ECC-1	luminal epithelium:	n/a	n/a
19	CTCF	chr13:48878177-48878338	MCF-7	breast:	n/a	chr13:48878298-48878311 chr13:48878295-48878308
20	ZNF143	chr13:48877624-48878346	GM12878	blood:	n/a	n/a
21	POLR2A	chr13:48877067-48878439	SK-N-MC	brain:	n/a	n/a
22	HCFC1	chr13:48877308-48878315	K562	blood:	n/a	n/a
23	CTCF	chr13:48878280-48878430	HRE	kidney:	n/a	chr13:48878298-48878311 chr13:48878295-48878308
24	TAF1	chr13:48877320-48878310	K562	blood:	n/a	n/a
25	CTCF	chr13:48878160-48878310	SK-N-SH_RA	brain:	n/a	chr13:48878295-48878308
26	HEY1	chr13:48877268-48878318	K562	blood:	n/a	n/a
27	MYC	chr13:48877440-48878303	K562	blood:	n/a	n/a
28	MXI1	chr13:48878231-48878343	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr13:48876411-48880767	GM12891	blood:	n/a	n/a
30	POLR2A	chr13:48877175-48879540	GM19193	blood:	n/a	n/a
31	MAX	chr13:48877314-48878883	Hela-S3	cervix:	n/a	chr13:48878320-48878330
32	POLR2A	chr13:48876718-48879287	IMR90	lung:	n/a	n/a
33	CTCF	chr13:48878180-48878330	HUVEC	blood vessel:	n/a	chr13:48878298-48878311 chr13:48878295-48878308
34	MAX	chr13:48877410-48878447	HepG2	liver:	n/a	chr13:48878320-48878330
35	POLR2A	chr13:48877126-48878433	K562	blood:	n/a	n/a
36	CTCF	chr13:48878180-48878330	GM12871	blood:	n/a	chr13:48878298-48878311 chr13:48878295-48878308
37	MAX	chr13:48877369-48878453	HepG2	liver:	n/a	chr13:48878320-48878330
38	EP300	chr13:48877369-48878486	ECC-1	luminal epithelium:	n/a	chr13:48877879-48877895
39	POLR2A	chr13:48876695-48879724	GM19099	blood:	n/a	n/a
40	CREB1	chr13:48877468-48878302	H1-hESC	embryonic stem cell:	n/a	n/a
41	CCNT2	chr13:48877471-48878350	K562	blood:	n/a	n/a
42	CREB1	chr13:48877433-48878391	A549	lung:	n/a	n/a
43	POLR2A	chr13:48877095-48878306	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr13:48877217-48878375	HEK293	kidney:	n/a	n/a
45	CTCF	chr13:48878220-48878370	SAEC	small airway:	n/a	chr13:48878298-48878311 chr13:48878295-48878308
46	POLR2A	chr13:48877532-48878443	GM12878	blood:	n/a	n/a
47	GATA1	chr13:48877203-48878324	PBDE	blood:	n/a	n/a
48	MAZ	chr13:48877037-48879206	IMR90	lung:	n/a	chr13:48878320-48878330
49	POLR2A	chr13:48877260-48879134	GM18526	blood:	n/a	n/a
50	MYC	chr13:48877147-48878687	K562	blood:	n/a	chr13:48878320-48878330

No.	Distal block	Cell Line	Cell type
1	chr13:48806118..48810225-chr13:48876144..48879386,12	MCF-7	breast:
2	chr13:48877684..48878312-chr17:7387237..7388144,2	Hela-S3	cervix:
3	chr13:48806544..48809798-chr13:48876519..48878974,4	K562	blood:
4	chr13:48876409..48879041-chr13:48891404..48895274,4	K562	blood:
5	chr13:48877598..48878598-chr2:139258866..139259815,3	HCT-116	colon:
6	chr13:48806625..48809806-chr13:48877426..48879405,3	K562	blood:
7	chr10:17269997..17270593-chr13:48877834..48878450,2	Hela-S3	cervix:
8	chr13:48611797..48612338-chr13:48877851..48878728,2	K562	blood:

Variant related genes	Relation type
LINC00441	TF binding region
ENSG00000228043	Chromatin interaction
ENSG00000144228	Chromatin interaction
ENSG00000026025	Chromatin interaction
ENSG00000136156	Chromatin interaction
ENSG00000136143	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000238086	Chromatin interaction
ENSG00000174282	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1981434	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1981435	0.88[ASN][1000 genomes]
rs3825417	0.86[ASN][1000 genomes]
rs4594153	0.81[EUR][1000 genomes]
rs9535007	0.81[EUR][1000 genomes]
rs9568029	0.81[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	esv3437840	chr13:48876976-48879524	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2252544	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48876400-48879200	Active TSS	Stomach Smooth Muscle	stomach
2	chr13:48876600-48878600	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr13:48876600-48878800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr13:48876600-48879000	Active TSS	Fetal Kidney	kidney
5	chr13:48876600-48879000	Active TSS	GM12878-XiMat	blood
6	chr13:48876600-48879200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:48876600-48879400	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr13:48876800-48878600	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr13:48876800-48878800	Active TSS	Brain Anterior Caudate	brain
10	chr13:48876800-48879000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr13:48876800-48879000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr13:48876800-48879200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr13:48876800-48879200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr13:48876800-48879200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:48876800-48879200	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr13:48876800-48879400	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr13:48876800-48879400	Active TSS	Colonic Mucosa	Colon
18	chr13:48876800-48879400	Active TSS	A549	lung
19	chr13:48876800-48879800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr13:48876800-48880000	Active TSS	K562	blood
21	chr13:48876800-48880200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:48877000-48878800	Active TSS	Duodenum Mucosa	Duodenum
23	chr13:48877000-48879000	Active TSS	H9 Cell Line	embryonic stem cell
24	chr13:48877000-48879000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr13:48877000-48879000	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr13:48877000-48879000	Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr13:48877000-48879000	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr13:48877000-48879200	Active TSS	Fetal Intestine Small	intestine
29	chr13:48877000-48879200	Active TSS	Fetal Stomach	stomach
30	chr13:48877000-48879200	Active TSS	Fetal Thymus	thymus
31	chr13:48877000-48879600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr13:48877000-48879600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr13:48877000-48879600	Active TSS	Psoas Muscle	Psoas
34	chr13:48877000-48879600	Active TSS	Right Ventricle	heart
35	chr13:48877000-48879800	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr13:48877000-48879800	Active TSS	Fetal Muscle Leg	muscle
37	chr13:48877000-48879800	Active TSS	Right Atrium	heart
38	chr13:48877000-48880000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr13:48877000-48880000	Active TSS	HSMMtube	muscle
40	chr13:48877000-48880200	Active TSS	Muscle Satellite Cultured Cells	--
41	chr13:48877000-48880200	Active TSS	NHLF	lung
42	chr13:48877200-48878600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr13:48877200-48878800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr13:48877200-48878800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:48877200-48878800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr13:48877200-48878800	Active TSS	Brain Cingulate Gyrus	brain
47	chr13:48877200-48878800	Active TSS	Brain Hippocampus Middle	brain
48	chr13:48877200-48878800	Active TSS	Fetal Intestine Large	intestine
49	chr13:48877200-48878800	Active TSS	Fetal Lung	lung
50	chr13:48877200-48878800	Active TSS	Placenta Amnion	Placenta Amnion

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