Variant report

Variant	rs561080616
Chromosome Location	chr1:227505427-227505428
allele	C/G
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	GTF2F1	chr1:227505281-227505644	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:227505289-227507173	ProgFib	skin:	n/a	n/a
3	CTCF	chr1:227505360-227505510	HAc	cerebellar:	n/a	n/a
4	MAX	chr1:227505325-227505721	A549	lung:	n/a	chr1:227505659-227505669
5	CCNT2	chr1:227505228-227506682	K562	blood:	n/a	chr1:227506372-227506381
6	MAFK	chr1:227505183-227505637	IMR90	lung:	n/a	n/a
7	CTCF	chr1:227505380-227505530	AoAF	blood vessel:	n/a	n/a
8	FOS	chr1:227505125-227505473	MCF10A-Er-Src	breast:	n/a	n/a
9	CUX1	chr1:227505263-227505592	K562	blood:	n/a	n/a
10	SIN3AK20	chr1:227505194-227505650	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr1:227505368-227507144	K562	blood:	n/a	n/a
12	HEY1	chr1:227505309-227507056	K562	blood:	n/a	chr1:227505900-227505915 chr1:227505654-227505669 chr1:227506721-227506736 chr1:227506549-227506564 chr1:227505897-227505912 chr1:227505819-227505834
13	POLR2A	chr1:227504780-227506688	Hela-S3	cervix:	n/a	n/a
14	ZC3H11A	chr1:227505401-227505574	K562	blood:	n/a	n/a
15	POLR2A	chr1:227505416-227507157	GM19193	blood:	n/a	n/a
16	CTCF	chr1:227505378-227505502	Fibrobl	skin:	n/a	n/a
17	MXI1	chr1:227504799-227505595	Hela-S3	cervix:	n/a	n/a
18	HA-E2F1	chr1:227505284-227506944	MCF-7	breast:	n/a	chr1:227505900-227505910 chr1:227505905-227505914 chr1:227505653-227505662 chr1:227505461-227505468 chr1:227505461-227505468 chr1:227505461-227505468
19	CTCF	chr1:227505340-227505490	SAEC	small airway:	n/a	n/a
20	CTCF	chr1:227505320-227505470	BE2_C	brain:	n/a	n/a
21	SIN3A	chr1:227504748-227507247	H1-hESC	embryonic stem cell:	n/a	chr1:227505012-227505021 chr1:227506503-227506512
22	STAT3	chr1:227505124-227505577	MCF10A-Er-Src	breast:	n/a	chr1:227505328-227505339 chr1:227505355-227505363 chr1:227505324-227505344 chr1:227505463-227505475
23	MYC	chr1:227505354-227505638	MCF10A-Er-Src	breast:	n/a	n/a
24	MAFK	chr1:227505258-227505541	K562	blood:	n/a	n/a
25	GATA2	chr1:227505243-227505628	SH-SY5Y	brain:	n/a	n/a
26	EP300	chr1:227504677-227505627	K562	blood:	n/a	chr1:227505214-227505228 chr1:227505284-227505298 chr1:227505213-227505227 chr1:227505340-227505354 chr1:227505215-227505229
27	CTCF	chr1:227505280-227505430	AG04450	lung:	n/a	n/a
28	CTCF	chr1:227505340-227505490	AoAF	blood vessel:	n/a	n/a
29	ZBTB7A	chr1:227505329-227506982	K562	blood:	n/a	chr1:227505472-227505481 chr1:227505745-227505756 chr1:227506007-227506016 chr1:227505746-227505757
30	POLR2A	chr1:227505353-227505578	A549	lung:	n/a	n/a
31	RAD21	chr1:227505251-227505506	A549	lung:	n/a	n/a
32	POLR2A	chr1:227504718-227507432	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr1:227505380-227505531	A549	lung:	n/a	n/a
34	TAF1	chr1:227505277-227507245	H1-hESC	embryonic stem cell:	n/a	n/a
35	CEBPB	chr1:227505117-227505491	IMR90	lung:	n/a	chr1:227505283-227505294
36	CTCF	chr1:227505340-227505490	HepG2	liver:	n/a	n/a
37	CTCF	chr1:227505320-227505470	BJ	skin:	n/a	n/a
38	MAX	chr1:227504749-227505748	Hela-S3	cervix:	n/a	chr1:227505313-227505322 chr1:227505659-227505669
39	CEBPB	chr1:227503465-227506205	Hela-S3	cervix:	n/a	chr1:227505283-227505294
40	CTCF	chr1:227505252-227505607	K562	blood:	n/a	n/a
41	TAF1	chr1:227505293-227507153	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF1	chr1:227505137-227505554	SK-N-SH	brain:	n/a	n/a
43	CTCF	chr1:227505389-227505523	A549	lung:	n/a	n/a
44	CTCF	chr1:227505340-227505490	HBMEC	blood vessel:	n/a	n/a
45	FOS	chr1:227504770-227505504	MCF10A-Er-Src	breast:	n/a	n/a
46	GATA3	chr1:227505190-227505614	T-47D	breast:	n/a	n/a
47	MAFK	chr1:227505224-227505589	Hela-S3	cervix:	n/a	n/a
48	EP300	chr1:227505223-227505545	HepG2	liver:	n/a	chr1:227505284-227505298 chr1:227505340-227505354
49	JUN	chr1:227505332-227505607	K562	blood:	n/a	n/a
50	SMARCB1	chr1:227505319-227506806	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227365298..227367002-chr1:227505047..227506997,2	K562	blood:
2	chr1:227125150..227128196-chr1:227505421..227508280,4	MCF-7	breast:
3	chr1:227126362..227128612-chr1:227504788..227507568,2	MCF-7	breast:
4	chr1:227505349..227507259-chr17:61552926..61555906,2	MCF-7	breast:
5	chr1:227500962..227504758-chr1:227504964..227507747,3	MCF-7	breast:
6	chr1:227504778..227506670-chr1:227579538..227582289,3	K562	blood:
7	chr1:227504042..227507688-chr1:227616722..227620233,4	K562	blood:
8	chr1:227505302..227507077-chr1:227617949..227620450,2	MCF-7	breast:
9	chr1:227504778..227506536-chr1:227579859..227582289,2	K562	blood:

Variant related genes	Relation type
CDC42BPA	TF binding region
ENSG00000159640	Chromatin interaction
ENSG00000163050	Chromatin interaction
ENSG00000242757	Chromatin interaction
ENSG00000143776	Chromatin interaction
ENSG00000234277	Chromatin interaction
ENSG00000228625	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv3390376	chr1:227505104-227507452	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227500800-227506600	Active TSS	K562	blood
2	chr1:227501400-227506800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:227501400-227507000	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr1:227501600-227507000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:227501800-227505600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:227501800-227505800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:227501800-227506600	Active TSS	Fetal Stomach	stomach
8	chr1:227501800-227506600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr1:227501800-227506600	Active TSS	HMEC	breast
10	chr1:227501800-227506600	Active TSS	NHEK	skin
11	chr1:227501800-227506800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:227501800-227506800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:227501800-227506800	Active TSS	Brain Anterior Caudate	brain
14	chr1:227501800-227506800	Active TSS	A549	lung
15	chr1:227501800-227506800	Active TSS	NHLF	lung
16	chr1:227501800-227507000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:227501800-227507000	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:227501800-227507000	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr1:227501800-227507000	Active TSS	Fetal Kidney	kidney
20	chr1:227501800-227507200	Active TSS	Duodenum Mucosa	Duodenum
21	chr1:227501800-227507200	Active TSS	NHDF-Ad	bronchial
22	chr1:227502000-227506600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:227502000-227506600	Active TSS	Muscle Satellite Cultured Cells	--
24	chr1:227502000-227506600	Active TSS	Colonic Mucosa	Colon
25	chr1:227502000-227506600	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr1:227502000-227506600	Active TSS	HUVEC	blood vessel
27	chr1:227502000-227506800	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr1:227502000-227506800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:227502000-227506800	Active TSS	Stomach Smooth Muscle	stomach
30	chr1:227502000-227506800	Active TSS	NH-A	brain
31	chr1:227502000-227507000	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr1:227502000-227507000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr1:227502000-227507000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:227502000-227507000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:227502000-227507000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:227502000-227507000	Active TSS	Brain Angular Gyrus	brain
37	chr1:227502000-227507000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:227502000-227507000	Active TSS	Brain Substantia Nigra	brain
39	chr1:227502000-227507000	Active TSS	HSMMtube	muscle
40	chr1:227502000-227507200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:227502000-227507200	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr1:227502000-227507200	Active TSS	Psoas Muscle	Psoas
43	chr1:227502200-227505600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:227502200-227506800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:227502200-227506800	Active TSS	Brain Cingulate Gyrus	brain
46	chr1:227502200-227506800	Active TSS	Fetal Muscle Leg	muscle
47	chr1:227502200-227507000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:227502200-227507200	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr1:227502200-227507600	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr1:227502400-227507000	Active TSS	H1 Cell Line	embryonic stem cell

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