Variant report

Variant	rs11001560
Chromosome Location	chr10:54075127-54075128
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	MAX	chr10:54073032-54075312	A549	lung:	n/a	n/a
2	POLR2A	chr10:54072994-54075187	MCF-7	breast:	n/a	n/a
3	FOSL2	chr10:54074994-54076093	A549	lung:	n/a	chr10:54075935-54075944 chr10:54075724-54075734 chr10:54075724-54075734
4	POLR2A	chr10:54073615-54076920	HUVEC	blood vessel:	n/a	n/a
5	MAZ	chr10:54073295-54075277	IMR90	lung:	n/a	n/a
6	POLR2A	chr10:54074935-54075198	HepG2	liver:	n/a	n/a
7	REST	chr10:54072922-54075349	A549	lung:	n/a	chr10:54073933-54073946
8	POLR2A	chr10:54072977-54075692	Gliobla	brain:	n/a	n/a
9	SP1	chr10:54073169-54075305	A549	lung:	n/a	chr10:54074927-54074937 chr10:54074910-54074919 chr10:54074913-54074927 chr10:54074927-54074936 chr10:54074926-54074938 chr10:54074905-54074914 chr10:54074909-54074921 chr10:54074923-54074937 chr10:54074911-54074920 chr10:54074926-54074938 chr10:54074910-54074920 chr10:54074909-54074921
10	POLR2A	chr10:54075111-54075415	HepG2	liver:	n/a	n/a
11	JUND	chr10:54073611-54075480	A549	lung:	n/a	n/a
12	POLR2A	chr10:54073464-54075557	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr10:54073525-54079363	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr10:54073092-54080655	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr10:54073646-54075420	MCF10A-Er-Src	breast:	n/a	n/a
16	GATA3	chr10:54073034-54075851	A549	lung:	n/a	chr10:54075334-54075351 chr10:54075069-54075076 chr10:54075068-54075078
17	POLR2A	chr10:54074915-54076802	HCT-116	colon:	n/a	n/a
18	POLR2A	chr10:54074939-54075701	SK-N-SH	brain:	n/a	n/a
19	HEY1	chr10:54073574-54076765	HepG2	liver:	n/a	n/a
20	PML	chr10:54074956-54075405	MCF-7	breast:	n/a	n/a
21	GATA3	chr10:54072834-54077297	SK-N-SH	brain:	n/a	chr10:54076036-54076046 chr10:54075334-54075351 chr10:54075069-54075076 chr10:54075068-54075078
22	BCL3	chr10:54072807-54075220	A549	lung:	n/a	chr10:54074906-54074919 chr10:54074911-54074920
23	MAX	chr10:54073616-54075200	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr10:54074915-54075266	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr10:54072864-54080901	ProgFib	skin:	n/a	n/a
26	MAX	chr10:54073638-54075197	SK-N-SH	brain:	n/a	n/a
27	MAX	chr10:54072918-54075448	A549	lung:	n/a	chr10:54075399-54075409
28	BCL3	chr10:54074833-54076941	A549	lung:	n/a	chr10:54074906-54074919 chr10:54074911-54074920
29	POLR2A	chr10:54074945-54078566	HepG2	liver:	n/a	n/a
30	SIN3AK20	chr10:54072955-54075835	MCF-7	breast:	n/a	n/a
31	TAF1	chr10:54073206-54076883	A549	lung:	n/a	n/a
32	CTCF	chr10:54072767-54075403	SK-N-SH	brain:	n/a	chr10:54073933-54073946
33	GTF2F1	chr10:54073641-54075143	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr10:54072740-54080656	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr10:54073229-54079826	HUVEC	blood vessel:	n/a	n/a
36	TCF12	chr10:54072631-54080026	A549	lung:	n/a	n/a
37	USF1	chr10:54073324-54077167	A549	lung:	n/a	chr10:54074078-54074094
38	SMC3	chr10:54073573-54075219	Hela-S3	cervix:	n/a	chr10:54074966-54074976
39	STAT3	chr10:54075035-54075179	MCF10A-Er-Src	breast:	n/a	n/a
40	MAX	chr10:54074984-54075152	A549	lung:	n/a	n/a
41	POLR2A	chr10:54073758-54075132	Hela-S3	cervix:	n/a	n/a
42	SP1	chr10:54072902-54075325	A549	lung:	n/a	chr10:54074927-54074937 chr10:54074910-54074919 chr10:54074913-54074927 chr10:54074927-54074936 chr10:54074926-54074938 chr10:54074905-54074914 chr10:54074909-54074921 chr10:54074923-54074937 chr10:54074911-54074920 chr10:54074926-54074938 chr10:54074910-54074920 chr10:54074909-54074921
43	POLR2A	chr10:54072772-54079176	HCT-116	colon:	n/a	n/a
44	TCF7L2	chr10:54075031-54075665	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr10:54073363-54076907	MCF-7	breast:	n/a	n/a
46	HA-E2F1	chr10:54072841-54075311	MCF-7	breast:	n/a	chr10:54074910-54074919 chr10:54072915-54072924
47	TAF1	chr10:54073511-54075168	SK-N-SH	brain:	n/a	n/a
48	CHD1	chr10:54073374-54076258	IMR90	lung:	n/a	chr10:54075436-54075446
49	POLR2A	chr10:54074946-54075183	HCT-116	colon:	n/a	n/a
50	POLR2A	chr10:54072679-54080064	HUVEC	blood vessel:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:54075082-54075132	HCF	heart:	n/a
2	chr10:54075082-54075132	Hepatocyte	liver:	n/a
3	chr10:54075082-54075132	Caco-2	colon:	n/a
4	chr10:54075082-54075132	RPTEC	kidney:	n/a
5	chr10:54075082-54075132	MCF10A-Er-Src	breast:	n/a
6	chr10:54075082-54075132	HCM	heart:	n/a
7	chr10:54075082-54075132	GM12892	blood:	n/a
8	chr10:54075082-54075132	MCF-7	breast:	n/a
9	chr10:54075082-54075132	HEK293	kidney:	embryo
10	chr10:54075082-54075132	PANC-1	pancreas:	n/a
11	chr10:54075082-54075132	H1-hESC	embryonic stem cell:	embryo
12	chr10:54075082-54075132	A549	lung:	n/a
13	chr10:54075082-54075132	SK-N-MC	brain:	n/a
14	chr10:54075082-54075132	HRPEpiC	eye:	n/a
15	chr10:54075082-54075132	U87	brain:	n/a
16	chr10:54075082-54075132	BE2_C	brain:	n/a
17	chr10:54075082-54075132	CMK	blood:	n/a
18	chr10:54075082-54075132	NT2-D1	testis:	n/a
19	chr10:54075082-54075132	SAEC	small airway:	n/a
20	chr10:54075082-54075132	AG09309	skin:	n/a
21	chr10:54075082-54075132	NHDF-neo	bronchial:	n/a
22	chr10:54075082-54075132	HNPCEpiC	eye:	n/a
23	chr10:54075082-54075132	GM19239	blood:	n/a
24	chr10:54075082-54075132	SKMC	muscle:	n/a
25	chr10:54075082-54075132	BJ	skin:	n/a
26	chr10:54075082-54075132	HMEC	breast:	n/a
27	chr10:54075082-54075132	SK-N-SH_RA	brain:	n/a
28	chr10:54075082-54075132	NH-A	brain:	n/a
29	chr10:54075082-54075132	PFSK-1	brain:	n/a
30	chr10:54075082-54075132	AG09319	gingival:	n/a
31	chr10:54075082-54075132	ProgFib	skin:	n/a
32	chr10:54075082-54075132	ECC-1	luminal epithelium:	n/a
33	chr10:54075082-54075132	ovcar-3	ovarian:	n/a
34	chr10:54075082-54075132	HCT-116	colon:	n/a
35	chr10:54075082-54075132	HUVEC	blood vessel:	n/a
36	chr10:54075082-54075132	HIPEpiC	eye:	n/a
37	chr10:54075082-54075132	Jurkat	blood:	n/a
38	chr10:54075082-54075132	NB4	blood:	n/a
39	chr10:54075082-54075132	GM12891	blood:	n/a
40	chr10:54075082-54075132	HepG2	liver:	n/a
41	chr10:54075082-54075132	AG04450	lung:	fetal
42	chr10:54075082-54075132	HAEpiC	amniotic membrane:	n/a
43	chr10:54075082-54075132	HRCEpiC	kidney:	n/a
44	chr10:54075082-54075132	IMR90	lung:	fetal
45	chr10:54075082-54075132	HEEpiC	esophagus:	n/a
46	chr10:54075082-54075132	AoSMC	blood vessel:	n/a
47	chr10:54075082-54075132	HPAEpiC	pulmonary alveolar:	n/a
48	chr10:54075082-54075132	AG10803	skin:	n/a
49	chr10:54075082-54075132	PrEC	prostate:	n/a
50	chr10:54075082-54075132	GM06990	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:54065577..54083492-chr10:54193846..54218961,120	MCF-7	breast:
2	chr10:54073525..54075924-chr10:54146848..54149629,2	MCF-7	breast:
3	chr10:54073396..54076476-chr10:54227833..54231095,3	MCF-7	breast:
4	chr10:54073032..54076598-chr10:54229475..54234592,10	MCF-7	breast:
5	chr10:54071324..54082180-chr10:54192987..54217560,81	MCF-7	breast:

Variant related genes	Relation type
PRKG1-AS1	TF binding region
PRKG1-AS1	CpG island
ENSG00000213657	Chromatin interaction
ENSG00000231131	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10733905	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10824381	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs1569199	0.80[EUR][1000 genomes]
rs2241529	0.93[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7087520	0.80[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv895400	chr10:54073294-54094359	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54072800-54075200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr10:54072800-54075200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr10:54072800-54075800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr10:54072800-54075800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr10:54073000-54075800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr10:54073200-54075800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:54073400-54075200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr10:54073400-54075400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr10:54073400-54075600	Active TSS	Brain Cingulate Gyrus	brain
10	chr10:54073400-54075800	Active TSS	HSMM	muscle
11	chr10:54073400-54075800	Active TSS	NHDF-Ad	bronchial
12	chr10:54073400-54076000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:54073400-54076200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:54073400-54076600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:54073600-54075200	Active TSS	HMEC	breast
16	chr10:54073600-54075400	Active TSS	HUVEC	blood vessel
17	chr10:54073600-54075600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:54073600-54075600	Active TSS	HSMMtube	muscle
19	chr10:54073600-54075800	Active TSS	NH-A	brain
20	chr10:54073600-54075800	Active TSS	NHLF	lung
21	chr10:54073600-54077000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr10:54073800-54075200	Active TSS	Brain Angular Gyrus	brain
23	chr10:54073800-54075200	Active TSS	Brain Anterior Caudate	brain
24	chr10:54073800-54075200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr10:54073800-54075200	Active TSS	Brain Substantia Nigra	brain
26	chr10:54073800-54075200	Bivalent/Poised TSS	Fetal Lung	lung
27	chr10:54073800-54075400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr10:54073800-54075400	Active TSS	Osteobl	bone
29	chr10:54073800-54076000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr10:54074200-54077000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr10:54074400-54075200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr10:54074400-54076000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:54074400-54077400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
34	chr10:54074600-54075400	Bivalent/Poised TSS	Fetal Brain Female	brain
35	chr10:54074800-54075200	Bivalent Enhancer	Primary T cells from cord blood	blood
36	chr10:54074800-54075200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
37	chr10:54074800-54075200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:54074800-54075200	Active TSS	Brain Hippocampus Middle	brain
39	chr10:54074800-54075200	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr10:54074800-54075200	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr10:54074800-54075400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr10:54074800-54075400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr10:54074800-54075400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:54074800-54075400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr10:54074800-54075400	Bivalent/Poised TSS	HepG2	liver
46	chr10:54074800-54075600	Active TSS	Right Ventricle	heart
47	chr10:54074800-54075800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr10:54074800-54076400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr10:54074800-54076400	Active TSS	Placenta	Placenta
50	chr10:54074800-54076600	Active TSS	Fetal Kidney	kidney

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