Variant report

Variant	rs561586826
Chromosome Location	chr1:215740359-215740360
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	chr1:215740166-215741879	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:215740199-215741578	HepG2	liver:	n/a	n/a
3	RUNX3	chr1:215740290-215740993	GM12878	blood:	n/a	n/a
4	BACH1	chr1:215740321-215740761	H1-hESC	embryonic stem cell:	n/a	n/a
5	PML	chr1:215740231-215741823	MCF-7	breast:	n/a	n/a
6	GATA3	chr1:215740235-215741289	MCF-7	breast:	n/a	n/a
7	POLR2A	chr1:215740324-215740914	HepG2	liver:	n/a	n/a
8	TEAD4	chr1:215740304-215740812	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr1:215740314-215741818	Hela-S3	cervix:	n/a	chr1:215740902-215740912
10	GATA3	chr1:215740063-215740957	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr1:215740316-215741468	A549	lung:	n/a	n/a
12	FOS	chr1:215740196-215740687	MCF10A-Er-Src	breast:	n/a	n/a
13	CUX1	chr1:215740119-215740728	K562	blood:	n/a	n/a
14	MAX	chr1:215740186-215741888	MCF-7	breast:	n/a	chr1:215740902-215740912
15	POLR2A	chr1:215740322-215741497	K562	blood:	n/a	n/a
16	PML	chr1:215740229-215741695	GM12878	blood:	n/a	n/a
17	FOXA2	chr1:215740224-215740542	HepG2	liver:	n/a	n/a
18	CEBPB	chr1:215740158-215740868	MCF-7	breast:	n/a	n/a
19	POLR2A	chr1:215740330-215741508	GM12878	blood:	n/a	n/a
20	NR2F2	chr1:215739989-215740944	K562	blood:	n/a	n/a
21	MXI1	chr1:215739872-215741847	IMR90	lung:	n/a	n/a
22	POLR2A	chr1:215740061-215741717	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr1:215740297-215741534	Gliobla	brain:	n/a	n/a
24	POLR2A	chr1:215740271-215741532	GM15510	blood:	n/a	n/a
25	TBP	chr1:215740037-215742064	K562	blood:	n/a	n/a
26	FOXA1	chr1:215740142-215740667	T-47D	breast:	n/a	chr1:215740192-215740204 chr1:215740386-215740401
27	GATA2	chr1:215740196-215740742	HUVEC	blood vessel:	n/a	n/a
28	SP1	chr1:215740049-215740909	A549	lung:	n/a	chr1:215740494-215740501 chr1:215740492-215740506 chr1:215740860-215740869 chr1:215740859-215740871
29	POLR2A	chr1:215740341-215741805	HepG2	liver:	n/a	n/a
30	RELA	chr1:215740277-215741728	GM15510	blood:	n/a	n/a
31	POLR2A	chr1:215740345-215741855	K562	blood:	n/a	n/a
32	E2F4	chr1:215740298-215741426	K562	blood:	n/a	n/a
33	ZKSCAN1	chr1:215740301-215740814	Hela-S3	cervix:	n/a	n/a
34	GATA3	chr1:215740179-215740630	SH-SY5Y	brain:	n/a	n/a
35	CTCF	chr1:215740238-215740755	K562	blood:	n/a	n/a
36	REST	chr1:215740354-215740801	A549	lung:	n/a	chr1:215740610-215740623
37	POLR2A	chr1:215740327-215741637	ProgFib	skin:	n/a	n/a
38	MAX	chr1:215740312-215741554	K562	blood:	n/a	chr1:215740902-215740912
39	RCOR1	chr1:215740053-215740885	K562	blood:	n/a	n/a
40	MAX	chr1:215740290-215741635	HepG2	liver:	n/a	chr1:215740902-215740912
41	MXI1	chr1:215739867-215742249	SK-N-SH	brain:	n/a	n/a
42	TAF1	chr1:215740262-215740804	PFSK-1	brain:	n/a	n/a
43	TCF7L2	chr1:215740357-215741728	Hela-S3	cervix:	n/a	n/a
44	SMC3	chr1:215740338-215740675	GM12878	blood:	n/a	n/a
45	TFAP2A	chr1:215740159-215741617	Hela-S3	cervix:	n/a	chr1:215740966-215740974 chr1:215740966-215740974 chr1:215740591-215740602 chr1:215740966-215740974
46	E2F4	chr1:215739863-215740811	MCF10A-Er-Src	breast:	n/a	chr1:215740024-215740033
47	POLR2A	chr1:215740359-215741597	H1-hESC	embryonic stem cell:	n/a	n/a
48	MYC	chr1:215740288-215741761	MCF10A-Er-Src	breast:	n/a	chr1:215740902-215740912
49	TBP	chr1:215740065-215740792	Hela-S3	cervix:	n/a	n/a
50	FOXA2	chr1:215740270-215741108	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:215740294..215741084-chr19:3985081..3985884,2	Hela-S3	cervix:
2	chr1:215739388..215743068-chr1:215745972..215749293,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USH2A-1	chr1:215740146-215740734	NONHSAT009473

Variant related genes	Relation type
KCTD3	TF binding region
ENSG00000167658	Chromatin interaction
ENSG00000136636	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796390	chr1:215561548-215799074	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3411228	chr1:215704606-215742745	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3334079	chr1:215717606-215745691	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3362620	chr1:215739954-215742502	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215739400-215742200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:215739600-215742000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:215739800-215740400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:215739800-215740400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:215739800-215740400	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr1:215739800-215740400	Flanking Active TSS	HUVEC	blood vessel
7	chr1:215739800-215740600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:215739800-215742000	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr1:215739800-215742200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:215739800-215742200	Active TSS	Osteobl	bone
11	chr1:215739800-215742400	Active TSS	Muscle Satellite Cultured Cells	--
12	chr1:215739800-215742400	Active TSS	Brain Anterior Caudate	brain
13	chr1:215739800-215742600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:215739800-215742800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:215739800-215743200	Active TSS	A549	lung
16	chr1:215739800-215743200	Active TSS	NHDF-Ad	bronchial
17	chr1:215739800-215743400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:215739800-215743400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:215739800-215743600	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:215739800-215744400	Active TSS	NHLF	lung
21	chr1:215740000-215740400	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr1:215740000-215740400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr1:215740000-215740400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:215740000-215740400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr1:215740000-215740400	Flanking Active TSS	Brain Angular Gyrus	brain
26	chr1:215740000-215740400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr1:215740000-215740400	Flanking Active TSS	Dnd41	blood
28	chr1:215740000-215740400	Active TSS	HepG2	liver
29	chr1:215740000-215740400	Flanking Active TSS	NH-A	brain
30	chr1:215740000-215740600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr1:215740000-215740600	Active TSS	Right Atrium	heart
32	chr1:215740000-215741000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:215740000-215741000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:215740000-215741000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:215740000-215741200	Active TSS	Adipose Nuclei	Adipose
36	chr1:215740000-215741800	Active TSS	Placenta	Placenta
37	chr1:215740000-215742000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:215740000-215742000	Active TSS	Liver	Liver
39	chr1:215740000-215742000	Active TSS	Brain Germinal Matrix	brain
40	chr1:215740000-215742000	Active TSS	Fetal Brain Female	brain
41	chr1:215740000-215742000	Active TSS	Fetal Muscle Trunk	muscle
42	chr1:215740000-215742000	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr1:215740000-215742200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:215740000-215742200	Active TSS	Brain Cingulate Gyrus	brain
45	chr1:215740000-215742200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:215740000-215742200	Active TSS	Brain Substantia Nigra	brain
47	chr1:215740000-215742200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr1:215740000-215742200	Active TSS	Fetal Kidney	kidney
49	chr1:215740000-215742200	Active TSS	Fetal Stomach	stomach
50	chr1:215740000-215742200	Active TSS	Fetal Thymus	thymus

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