Variant report

Variant	rs2248907
Chromosome Location	chr1:47655816-47655817
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	STAT3	chr1:47655666-47656355	MCF10A-Er-Src	breast:	n/a	chr1:47655955-47655966 chr1:47656035-47656046
2	STAT3	chr1:47655686-47656321	MCF10A-Er-Src	breast:	n/a	chr1:47655955-47655966 chr1:47656035-47656046
3	MYC	chr1:47655703-47656315	MCF10A-Er-Src	breast:	n/a	chr1:47656026-47656036
4	STAT3	chr1:47655671-47656257	MCF10A-Er-Src	breast:	n/a	chr1:47655955-47655966 chr1:47656035-47656046
5	POLR2A	chr1:47655501-47656322	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:47655685-47656352	MCF10A-Er-Src	breast:	n/a	n/a
7	E2F6	chr1:47655570-47656117	A549	lung:	n/a	n/a
8	MYC	chr1:47655625-47656380	MCF10A-Er-Src	breast:	n/a	chr1:47656026-47656036
9	SP1	chr1:47655666-47656127	A549	lung:	n/a	chr1:47656026-47656036 chr1:47656025-47656037 chr1:47656026-47656036 chr1:47656026-47656035 chr1:47656025-47656037 chr1:47656027-47656036
10	STAT3	chr1:47655758-47656263	MCF10A-Er-Src	breast:	n/a	chr1:47655955-47655966 chr1:47656035-47656046
11	E2F4	chr1:47655776-47656279	MCF10A-Er-Src	breast:	n/a	chr1:47656177-47656192
12	E2F6	chr1:47655501-47656443	A549	lung:	n/a	chr1:47656177-47656192
13	MAX	chr1:47655766-47656364	Hela-S3	cervix:	n/a	chr1:47656026-47656036
14	POLR2A	chr1:47655736-47655847	MCF-7	breast:	n/a	n/a
15	FOS	chr1:47655683-47656262	MCF10A-Er-Src	breast:	n/a	n/a
16	SMARCB1	chr1:47655466-47656552	Hela-S3	cervix:	n/a	n/a
17	FOS	chr1:47655745-47656180	MCF10A-Er-Src	breast:	n/a	n/a
18	MAX	chr1:47655523-47656361	A549	lung:	n/a	chr1:47656026-47656036
19	MAX	chr1:47655783-47656203	A549	lung:	n/a	chr1:47656026-47656036
20	RCOR1	chr1:47655684-47656375	IMR90	lung:	n/a	n/a
21	FOS	chr1:47655704-47656208	MCF10A-Er-Src	breast:	n/a	n/a
22	MAZ	chr1:47655585-47656475	IMR90	lung:	n/a	chr1:47656026-47656036
23	MAX	chr1:47655403-47656532	A549	lung:	n/a	chr1:47656026-47656036
24	POLR2A	chr1:47655407-47656357	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47654478..47656007-chr1:47798811..47801587,2	MCF-7	breast:

Variant related genes	Relation type
PDZK1IP1	TF binding region
ENSG00000162368	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2251786	0.92[EUR][1000 genomes]
rs2798354	0.81[EUR][1000 genomes]
rs2821075	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4926718	0.93[TSI][hapmap]
rs6588655	0.82[CEU][hapmap]
rs71645854	0.84[AFR][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	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2248907	CMPK1	cis	lymphoblastoid	seeQTL
rs2248907	ATPAF1	cis	parietal	SCAN
rs2248907	PDZK1IP1	cis	Artery Aorta	GTEx
rs2248907	PDZK1IP1	cis	Artery Tibial	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47652600-47659000	Enhancers	Fetal Intestine Small	intestine
2	chr1:47652800-47658400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:47653200-47658400	Enhancers	K562	blood
4	chr1:47653600-47656600	Enhancers	HepG2	liver
5	chr1:47654600-47659200	Enhancers	Fetal Intestine Large	intestine
6	chr1:47655000-47656000	Flanking Active TSS	Stomach Mucosa	stomach
7	chr1:47655000-47656400	Flanking Active TSS	Pancreas	Pancrea
8	chr1:47655000-47656600	Enhancers	A549	lung
9	chr1:47655000-47659000	Enhancers	Lung	lung
10	chr1:47655000-47659200	Enhancers	Fetal Muscle Leg	muscle
11	chr1:47655200-47656000	Flanking Active TSS	Colonic Mucosa	Colon
12	chr1:47655200-47656000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr1:47655200-47656400	Enhancers	Right Atrium	heart
14	chr1:47655200-47658400	Enhancers	Fetal Muscle Trunk	muscle
15	chr1:47655200-47659000	Enhancers	Adipose Nuclei	Adipose
16	chr1:47655400-47656200	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr1:47655400-47656200	Enhancers	Hela-S3	cervix
18	chr1:47655400-47656600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:47655400-47657200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:47655400-47658200	Enhancers	HMEC	breast
21	chr1:47655400-47658800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:47655400-47659400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:47655600-47656000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:47655600-47656200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:47655600-47656600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr1:47655600-47656600	Bivalent Enhancer	Fetal Stomach	stomach
27	chr1:47655600-47656600	Enhancers	Ovary	ovary
28	chr1:47655600-47656600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr1:47655600-47656800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:47655600-47657000	Enhancers	Right Ventricle	heart
31	chr1:47655600-47657400	Enhancers	Spleen	Spleen
32	chr1:47655600-47657800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:47655600-47657800	Weak transcription	Small Intestine	intestine
34	chr1:47655600-47658600	Enhancers	NHEK	skin
35	chr1:47655600-47659000	Enhancers	Placenta	Placenta
36	chr1:47655600-47659000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:47655600-47659000	Enhancers	HSMMtube	muscle
38	chr1:47655600-47659200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr1:47655800-47656000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
40	chr1:47655800-47656000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:47655800-47656000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
42	chr1:47655800-47656000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:47655800-47656000	Flanking Active TSS	Gastric	stomach
44	chr1:47655800-47656000	Flanking Active TSS	Osteobl	bone
45	chr1:47655800-47656400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:47655800-47656400	Enhancers	Fetal Lung	lung
47	chr1:47655800-47656400	Enhancers	Rectal Smooth Muscle	rectum
48	chr1:47655800-47656400	Enhancers	NH-A	brain
49	chr1:47655800-47656600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
50	chr1:47655800-47656600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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