Variant report

Variant	rs11001553
Chromosome Location	chr10:54072901-54072902
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	YY1	chr10:54072882-54073256	SK-N-SH_RA	brain:	n/a	n/a
2	SPI1	chr10:54072825-54073283	HL-60	blood:	n/a	chr10:54073064-54073077 chr10:54073067-54073076 chr10:54073065-54073078
3	ARID3A	chr10:54072857-54074523	HepG2	liver:	n/a	n/a
4	GTF2F1	chr10:54072889-54072980	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr10:54072843-54073200	H1-hESC	embryonic stem cell:	n/a	chr10:54072861-54072870
6	GATA2	chr10:54072878-54074785	SH-SY5Y	brain:	n/a	n/a
7	CTCF	chr10:54072615-54075091	A549	lung:	n/a	chr10:54073933-54073946
8	GATA3	chr10:54072834-54077297	SK-N-SH	brain:	n/a	chr10:54076036-54076046 chr10:54075334-54075351 chr10:54075069-54075076 chr10:54075068-54075078
9	BCL3	chr10:54072807-54075220	A549	lung:	n/a	chr10:54074906-54074919 chr10:54074911-54074920
10	POLR2A	chr10:54072864-54080901	ProgFib	skin:	n/a	n/a
11	TCF7L2	chr10:54072515-54074594	HEK293	kidney:	n/a	chr10:54073942-54073956
12	CTCF	chr10:54072767-54075403	SK-N-SH	brain:	n/a	chr10:54073933-54073946
13	JUND	chr10:54072714-54073047	HepG2	liver:	n/a	chr10:54072861-54072870
14	GATA3	chr10:54072859-54075100	MCF-7	breast:	n/a	chr10:54075069-54075076 chr10:54075068-54075078
15	POLR2A	chr10:54072740-54080656	PANC-1	pancreas:	n/a	n/a
16	ZNF263	chr10:54072901-54074789	HEK293-T-REx	kidney:	n/a	chr10:54074158-54074179
17	TCF12	chr10:54072631-54080026	A549	lung:	n/a	n/a
18	KAP1	chr10:54072855-54074761	U2OS	brain:	n/a	n/a
19	JUN	chr10:54072726-54073036	HUVEC	blood vessel:	n/a	chr10:54072860-54072873 chr10:54072861-54072870
20	FOSL2	chr10:54072901-54074956	A549	lung:	n/a	n/a
21	POLR2A	chr10:54072772-54079176	HCT-116	colon:	n/a	n/a
22	TCF7L2	chr10:54072793-54074692	PANC-1	pancreas:	n/a	chr10:54073942-54073956
23	HA-E2F1	chr10:54072841-54075311	MCF-7	breast:	n/a	chr10:54074910-54074919 chr10:54072915-54072924
24	POLR2A	chr10:54072792-54074449	H1-neurons	neurons:	n/a	n/a
25	KAP1	chr10:54072874-54074776	HEK293	kidney:	n/a	n/a
26	EP300	chr10:54072802-54074945	A549	lung:	n/a	chr10:54074160-54074174 chr10:54072944-54072958
27	POLR2A	chr10:54072679-54080064	HUVEC	blood vessel:	n/a	n/a
28	JUN	chr10:54072706-54073054	HepG2	liver:	n/a	chr10:54072860-54072873 chr10:54072861-54072870
29	TCF7L2	chr10:54072883-54074820	HCT-116	colon:	n/a	chr10:54073942-54073956
30	POLR2A	chr10:54072716-54080807	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:54071543..54073516-chr10:54113139..54115614,2	MCF-7	breast:
2	chr10:54065577..54083492-chr10:54193846..54218961,120	MCF-7	breast:
3	chr10:54071324..54082180-chr10:54192987..54217560,81	MCF-7	breast:

Variant related genes	Relation type
DKK1	TF binding region
ENSG00000231131	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10762689	0.86[ASN][1000 genomes]
rs10824351	0.80[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11001548	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11001570	0.87[ASN][1000 genomes]
rs11001580	0.86[ASN][1000 genomes]
rs11001604	0.87[ASN][1000 genomes]
rs1590105	0.82[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs1991392	0.95[ASN][1000 genomes]
rs1991393	0.87[ASN][1000 genomes]
rs1991394	0.87[ASN][1000 genomes]
rs2288335	0.80[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs41281546	0.86[ASN][1000 genomes]
rs7073197	0.93[ASN][1000 genomes]
rs7081342	0.82[ASN][1000 genomes]
rs7083441	0.87[ASN][1000 genomes]
rs7910446	0.93[ASN][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	nsv1045692	chr10:53301450-54086823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv895399	chr10:53900872-54219820	Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54068400-54073000	Weak transcription	Hela-S3	cervix
2	chr10:54068800-54073000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:54068800-54073000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr10:54068800-54073000	Weak transcription	Gastric	stomach
5	chr10:54068800-54073000	Weak transcription	Left Ventricle	heart
6	chr10:54068800-54073000	Weak transcription	Pancreas	Pancrea
7	chr10:54068800-54073800	Weak transcription	Lung	lung
8	chr10:54069000-54073200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr10:54072600-54073200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr10:54072600-54073600	Flanking Active TSS	HMEC	breast
11	chr10:54072600-54075000	Active TSS	A549	lung
12	chr10:54072800-54073000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr10:54072800-54073000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
14	chr10:54072800-54073000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
15	chr10:54072800-54073000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:54072800-54073000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
17	chr10:54072800-54073000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:54072800-54073000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr10:54072800-54073000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr10:54072800-54073000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:54072800-54073000	Bivalent Enhancer	Primary T cells from cord blood	blood
22	chr10:54072800-54073000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:54072800-54073000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr10:54072800-54073000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:54072800-54073000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:54072800-54073000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr10:54072800-54073000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
28	chr10:54072800-54073000	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr10:54072800-54073000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
30	chr10:54072800-54073000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
31	chr10:54072800-54073000	Bivalent/Poised TSS	Fetal Kidney	kidney
32	chr10:54072800-54073000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
33	chr10:54072800-54073000	Active TSS	HSMM	muscle
34	chr10:54072800-54073000	Enhancers	HSMMtube	muscle
35	chr10:54072800-54073000	Active TSS	NHLF	lung
36	chr10:54072800-54073000	Active TSS	Osteobl	bone
37	chr10:54072800-54073200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr10:54072800-54073200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr10:54072800-54073200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr10:54072800-54073200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
41	chr10:54072800-54073200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:54072800-54073200	Bivalent Enhancer	Primary B cells from cord blood	blood
43	chr10:54072800-54073200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
44	chr10:54072800-54073200	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
45	chr10:54072800-54073200	Bivalent/Poised TSS	Fetal Lung	lung
46	chr10:54072800-54073400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
47	chr10:54072800-54073400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr10:54072800-54073400	Flanking Active TSS	NHDF-Ad	bronchial
49	chr10:54072800-54073600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr10:54072800-54073600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain

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