Variant report

Variant	rs595397
Chromosome Location	chr1:241804165-241804166
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	EP300	chr1:241803745-241806107	A549	lung:	n/a	chr1:241804139-241804149 chr1:241804154-241804164 chr1:241803841-241803857 chr1:241804622-241804636
2	POLR2A	chr1:241803145-241804337	K562	blood:	n/a	n/a
3	MAX	chr1:241802778-241804341	MCF-7	breast:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
4	MTA3	chr1:241803806-241804397	GM12878	blood:	n/a	n/a
5	CREB1	chr1:241802910-241804233	HepG2	liver:	n/a	n/a
6	E2F4	chr1:241803201-241804785	K562	blood:	n/a	chr1:241803839-241803848 chr1:241804035-241804044
7	BHLHE40	chr1:241803135-241804489	K562	blood:	n/a	n/a
8	EP300	chr1:241803780-241804274	HepG2	liver:	n/a	chr1:241804139-241804149 chr1:241804154-241804164 chr1:241803841-241803857
9	MAX	chr1:241803269-241805364	A549	lung:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
10	JUND	chr1:241803958-241805583	Hela-S3	cervix:	n/a	chr1:241805169-241805180
11	BCL3	chr1:241803712-241804889	A549	lung:	n/a	n/a
12	MAX	chr1:241803199-241805449	Hela-S3	cervix:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
13	FOSL2	chr1:241803746-241805666	A549	lung:	n/a	n/a
14	CHD2	chr1:241803105-241805505	Hela-S3	cervix:	n/a	chr1:241803837-241803847
15	JUN	chr1:241804122-241805483	Hela-S3	cervix:	n/a	n/a
16	MAFK	chr1:241803857-241805405	Hela-S3	cervix:	n/a	chr1:241804877-241804892 chr1:241805164-241805179
17	TBP	chr1:241803265-241804928	HepG2	liver:	n/a	n/a
18	MAX	chr1:241803459-241804192	K562	blood:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
19	POLR2A	chr1:241802347-241805302	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr1:241804030-241805438	MCF10A-Er-Src	breast:	n/a	chr1:241804179-241804199 chr1:241804951-241804958
21	POLR2A	chr1:241802916-241804172	K562	blood:	n/a	n/a
22	CEBPB	chr1:241803232-241805865	Hela-S3	cervix:	n/a	chr1:241804623-241804634 chr1:241804621-241804632 chr1:241804621-241804634 chr1:241804623-241804632
23	TBL1XR1	chr1:241803552-241804242	K562	blood:	n/a	n/a
24	MXI1	chr1:241803216-241805469	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:241802492-241804229	GM18951	blood:	n/a	n/a
26	RAD21	chr1:241804066-241805453	Hela-S3	cervix:	n/a	n/a
27	SP1	chr1:241803416-241806004	A549	lung:	n/a	chr1:241803838-241803852 chr1:241803942-241803956 chr1:241803838-241803848 chr1:241803839-241803848 chr1:241803837-241803849 chr1:241803707-241803718 chr1:241803838-241803847 chr1:241803740-241803751 chr1:241803838-241803848 chr1:241803696-241803707 chr1:241803838-241803847 chr1:241803837-241803849
28	ELK1	chr1:241803629-241805441	Hela-S3	cervix:	n/a	n/a
29	FOS	chr1:241803948-241805396	Hela-S3	cervix:	n/a	chr1:241805169-241805180
30	POLR2A	chr1:241803454-241804485	HepG2	liver:	n/a	n/a
31	E2F6	chr1:241803579-241805120	A549	lung:	n/a	chr1:241803839-241803848 chr1:241804035-241804044
32	HA-E2F1	chr1:241803185-241804657	MCF-7	breast:	n/a	chr1:241803839-241803848 chr1:241804035-241804044
33	POLR2A	chr1:241802710-241804788	HepG2	liver:	n/a	n/a
34	TFAP2C	chr1:241803198-241805402	Hela-S3	cervix:	n/a	chr1:241803895-241803910
35	SMC3	chr1:241803172-241805588	Hela-S3	cervix:	n/a	n/a
36	HEY1	chr1:241803021-241804275	HepG2	liver:	n/a	n/a
37	MAFK	chr1:241804107-241805353	HepG2	liver:	n/a	chr1:241804877-241804892 chr1:241805164-241805179
38	STAT3	chr1:241804011-241805462	MCF10A-Er-Src	breast:	n/a	chr1:241804179-241804199 chr1:241804951-241804958
39	POLR2A	chr1:241801599-241805416	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr1:241802932-241804993	HepG2	liver:	n/a	n/a
41	CHD1	chr1:241803112-241804321	IMR90	lung:	n/a	chr1:241803837-241803847
42	POLR2A	chr1:241802948-241804992	HepG2	liver:	n/a	n/a
43	ELK4	chr1:241803831-241804905	Hela-S3	cervix:	n/a	n/a
44	RCOR1	chr1:241802366-241804244	K562	blood:	n/a	n/a
45	MAX	chr1:241802801-241804320	H1-hESC	embryonic stem cell:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
46	MYC	chr1:241803392-241804308	HepG2	liver:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
47	POLR2A	chr1:241802313-241804306	K562	blood:	n/a	n/a
48	SMARCB1	chr1:241802469-241805865	Hela-S3	cervix:	n/a	n/a
49	MAX	chr1:241803261-241804856	HepG2	liver:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
50	E2F6	chr1:241802834-241804931	K562	blood:	n/a	chr1:241803839-241803848 chr1:241802963-241802975 chr1:241804035-241804044

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:241804128-241804178	GM19239	blood:	n/a
2	chr1:241804128-241804178	HL-60	blood:	n/a
3	chr1:241804128-241804178	SAEC	small airway:	n/a
4	chr1:241804128-241804178	HEEpiC	esophagus:	n/a
5	chr1:241804128-241804178	AG10803	skin:	n/a
6	chr1:241804128-241804178	AG09309	skin:	n/a
7	chr1:241804128-241804178	HMEC	breast:	n/a
8	chr1:241804128-241804178	HCT-116	colon:	n/a
9	chr1:241804128-241804178	ProgFib	skin:	n/a
10	chr1:241804128-241804178	HEK293	kidney:	embryo
11	chr1:241804128-241804178	AG04449	skin:	fetal
12	chr1:241804128-241804178	HCF	heart:	n/a
13	chr1:241804128-241804178	NH-A	brain:	n/a
14	chr1:241804128-241804178	U87	brain:	n/a
15	chr1:241804128-241804178	SK-N-SH	brain:	n/a
16	chr1:241804128-241804178	RPTEC	kidney:	n/a
17	chr1:241804128-241804178	GM12892	blood:	n/a
18	chr1:241804128-241804178	LNCaP	prostate:	n/a
19	chr1:241804128-241804178	AoSMC	blood vessel:	n/a
20	chr1:241804128-241804178	SKMC	muscle:	n/a
21	chr1:241804128-241804178	PFSK-1	brain:	n/a
22	chr1:241804128-241804178	HAEpiC	amniotic membrane:	n/a
23	chr1:241804128-241804178	NHBE	bronchial:	n/a
24	chr1:241804128-241804178	HCM	heart:	n/a
25	chr1:241804128-241804178	NHDF-neo	bronchial:	n/a
26	chr1:241804128-241804178	HepG2	liver:	n/a
27	chr1:241804128-241804178	HNPCEpiC	eye:	n/a
28	chr1:241804128-241804178	HRCEpiC	kidney:	n/a
29	chr1:241804128-241804178	NT2-D1	testis:	n/a
30	chr1:241804128-241804178	Jurkat	blood:	n/a
31	chr1:241804128-241804178	H1-hESC	embryonic stem cell:	embryo
32	chr1:241804128-241804178	HUVEC	blood vessel:	n/a
33	chr1:241804128-241804178	T-47D	breast:	n/a
34	chr1:241804128-241804178	K562	blood:	n/a
35	chr1:241804128-241804178	HIPEpiC	eye:	n/a
36	chr1:241804128-241804178	MCF-7	breast:	n/a
37	chr1:241804128-241804178	HPAEpiC	pulmonary alveolar:	n/a
38	chr1:241804128-241804178	HRE	kidney:	n/a
39	chr1:241804128-241804178	NB4	blood:	n/a
40	chr1:241804128-241804178	SK-N-MC	brain:	n/a
41	chr1:241804128-241804178	Hela-S3	cervix:	n/a
42	chr1:241804128-241804178	ECC-1	luminal epithelium:	n/a
43	chr1:241804128-241804178	HRPEpiC	eye:	n/a
44	chr1:241804128-241804178	Hepatocyte	liver:	n/a
45	chr1:241804128-241804178	GM06990	blood:	n/a
46	chr1:241804128-241804178	BE2_C	brain:	n/a
47	chr1:241804128-241804178	HCPEpiC	choroid plexus:	n/a
48	chr1:241804128-241804178	GM12878	blood:	n/a
49	chr1:241804128-241804178	AG04450	lung:	fetal
50	chr1:241804128-241804178	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:241803858..241804682-chr20:35723932..35724595,2	Hela-S3	cervix:
2	chr1:241693526..241696085-chr1:241801417..241805051,3	MCF-7	breast:
3	chr1:241799844..241805446-chr1:241909864..241915090,9	MCF-7	breast:
4	chr1:241801200..241805205-chr1:241910998..241914529,7	MCF-7	breast:
5	chr1:241797614..241799339-chr1:241801296..241804255,2	MCF-7	breast:
6	chr1:241803496..241804225-chr2:38978064..38978860,2	HCT-116	colon:
7	chr1:241802310..241805173-chr1:241993132..241995327,2	K562	blood:
8	chr1:241804081..241806043-chr1:241997998..241999955,2	MCF-7	breast:
9	chr1:241796724..241805103-chr1:242008052..242013159,15	K562	blood:
10	chr1:241799658..241805161-chr1:242010004..242013743,14	K562	blood:
11	chr1:241801957..241807032-chr1:241808533..241817679,11	K562	blood:

Variant related genes	Relation type
CHML	TF binding region
OPN3	TF binding region
CHML	CpG island
OPN3	CpG island
ENSG00000174371	Chromatin interaction
ENSG00000269846	Chromatin interaction
ENSG00000229022	Chromatin interaction
ENSG00000162843	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000117009	Chromatin interaction
ENSG00000080839	Chromatin interaction
ENSG00000203668	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2784165	0.89[AFR][1000 genomes]
rs598292	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs610693	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs613797	0.91[AFR][1000 genomes]
rs615141	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs616020	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs626437	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs626443	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs629088	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs630879	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs643321	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	esv3399692	chr1:241802554-241805102	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
11	esv3427336	chr1:241802829-241804677	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241799600-241804400	Active TSS	Brain Angular Gyrus	brain
2	chr1:241800400-241804200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:241801200-241804200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:241801200-241804200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:241801200-241804200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:241801200-241804200	Active TSS	Ovary	ovary
7	chr1:241801200-241804200	Active TSS	HSMM	muscle
8	chr1:241801800-241804200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:241801800-241804200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:241801800-241804200	Active TSS	Aorta	Aorta
11	chr1:241802000-241804200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:241802000-241804200	Active TSS	Muscle Satellite Cultured Cells	--
13	chr1:241802000-241804200	Active TSS	Thymus	Thymus
14	chr1:241802000-241804400	Active TSS	Fetal Brain Female	brain
15	chr1:241802000-241804400	Active TSS	Fetal Kidney	kidney
16	chr1:241802000-241804600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:241802200-241804200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:241802200-241804600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:241802400-241804200	Active TSS	Right Atrium	heart
20	chr1:241802600-241804200	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr1:241802600-241804200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:241802600-241804200	Active TSS	Brain Substantia Nigra	brain
23	chr1:241802600-241804200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr1:241802600-241804200	Active TSS	Osteobl	bone
25	chr1:241802600-241804400	Active TSS	Brain Anterior Caudate	brain
26	chr1:241802600-241804400	Active TSS	Rectal Smooth Muscle	rectum
27	chr1:241802600-241804600	Active TSS	Colon Smooth Muscle	Colon
28	chr1:241802800-241804200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:241802800-241804200	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr1:241802800-241804200	Active TSS	Esophagus	oesophagus
31	chr1:241802800-241804200	Active TSS	NHDF-Ad	bronchial
32	chr1:241803400-241804400	Active TSS	Brain Germinal Matrix	brain
33	chr1:241803600-241804800	Enhancers	Spleen	Spleen
34	chr1:241803800-241804200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:241803800-241804200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:241803800-241804200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:241803800-241804200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:241803800-241804200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr1:241803800-241804200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr1:241803800-241804200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr1:241803800-241804200	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr1:241803800-241804200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:241803800-241804200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:241803800-241804200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:241803800-241804200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:241803800-241804200	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr1:241803800-241804200	Flanking Active TSS	Pancreas	Pancrea
48	chr1:241803800-241804200	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr1:241803800-241804200	Flanking Active TSS	HMEC	breast
50	chr1:241803800-241804200	Flanking Active TSS	HUVEC	blood vessel

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