Variant report

Variant	rs539792152
Chromosome Location	chr1:62207906-62207907
allele	A/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	POLR2A	chr1:62207659-62208330	H1-hESC	embryonic stem cell:	n/a	n/a
2	NFIC	chr1:62207701-62208376	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr1:62207653-62209116	MCF-7	breast:	n/a	n/a
4	POLR2A	chr1:62207709-62208023	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:62207784-62208052	A549	lung:	n/a	n/a
6	ESR1	chr1:62207753-62208276	T-47D	breast:	n/a	n/a
7	TEAD4	chr1:62207769-62208189	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:62207698-62209183	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:62207807-62208194	Raji	blood:	n/a	n/a
10	POLR2A	chr1:62207121-62209260	Hela-S3	cervix:	n/a	n/a
11	SIN3AK20	chr1:62207883-62208024	HepG2	liver:	n/a	n/a
12	SIN3AK20	chr1:62207525-62208538	MCF-7	breast:	n/a	n/a
13	POLR2A	chr1:62207185-62209561	MCF10A-Er-Src	breast:	n/a	n/a
14	GATA3	chr1:62207580-62208110	MCF-7	breast:	n/a	chr1:62207735-62207745
15	REST	chr1:62207435-62208882	H1-neurons	neurons:	n/a	chr1:62208295-62208308
16	JUND	chr1:62207668-62208368	H1-hESC	embryonic stem cell:	n/a	chr1:62208351-62208360 chr1:62208355-62208364
17	MAX	chr1:62207841-62207994	HepG2	liver:	n/a	chr1:62207923-62207933
18	TAF7	chr1:62207905-62208382	H1-hESC	embryonic stem cell:	n/a	n/a
19	MYC	chr1:62207787-62207999	MCF-7	breast:	n/a	chr1:62207923-62207933
20	POLR2A	chr1:62207795-62208819	GM18526	blood:	n/a	n/a
21	TCF7L2	chr1:62207613-62208804	HCT-116	colon:	n/a	chr1:62207808-62207822
22	RCOR1	chr1:62207479-62208309	Hela-S3	cervix:	n/a	n/a
23	MAZ	chr1:62207781-62208842	GM12878	blood:	n/a	chr1:62207998-62208007 chr1:62207923-62207933
24	SIN3AK20	chr1:62207705-62208955	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr1:62207736-62208671	GM12892	blood:	n/a	n/a
26	POLR2A	chr1:62207733-62208921	GM19193	blood:	n/a	n/a
27	ZEB1	chr1:62207712-62208619	GM12878	blood:	n/a	chr1:62208160-62208169 chr1:62208121-62208130 chr1:62208122-62208129 chr1:62207978-62207989
28	BACH1	chr1:62207765-62207985	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr1:62207722-62208340	HCT-116	colon:	n/a	chr1:62207922-62207931
30	ZNF263	chr1:62207363-62209211	HEK293-T-REx	kidney:	n/a	n/a
31	POLR2A	chr1:62207833-62208859	A549	lung:	n/a	n/a
32	MAX	chr1:62207620-62208818	ECC-1	luminal epithelium:	n/a	chr1:62207998-62208007 chr1:62207923-62207933 chr1:62207695-62207704
33	MAX	chr1:62207415-62209080	Hela-S3	cervix:	n/a	chr1:62207998-62208007 chr1:62207923-62207933 chr1:62207582-62207591 chr1:62207695-62207704
34	POLR2A	chr1:62207745-62208919	GM18951	blood:	n/a	n/a
35	POLR2A	chr1:62207388-62209264	Hela-S3	cervix:	n/a	n/a
36	EGR1	chr1:62207814-62208362	H1-hESC	embryonic stem cell:	n/a	chr1:62208334-62208347 chr1:62207923-62207933 chr1:62207923-62207936 chr1:62207920-62207934 chr1:62208350-62208360
37	MAX	chr1:62207639-62209010	HepG2	liver:	n/a	chr1:62207998-62208007 chr1:62207923-62207933 chr1:62207695-62207704
38	GATA3	chr1:62207684-62208307	T-47D	breast:	n/a	chr1:62207735-62207745
39	ELF1	chr1:62207905-62208326	HepG2	liver:	n/a	n/a
40	CHD2	chr1:62207792-62209002	GM12878	blood:	n/a	chr1:62208102-62208112 chr1:62208348-62208358 chr1:62207920-62207930
41	TAF1	chr1:62207763-62208106	MCF-7	breast:	n/a	n/a
42	YY1	chr1:62207716-62208322	ECC-1	luminal epithelium:	n/a	chr1:62207922-62207931
43	POLR2A	chr1:62207718-62209059	HepG2	liver:	n/a	n/a
44	POLR2A	chr1:62207754-62208027	HepG2	liver:	n/a	n/a
45	HA-E2F1	chr1:62207586-62209165	MCF-7	breast:	n/a	chr1:62208350-62208359 chr1:62208295-62208305 chr1:62208462-62208471 chr1:62208795-62208805 chr1:62207922-62207931 chr1:62208334-62208344
46	MAX	chr1:62207773-62208397	H1-hESC	embryonic stem cell:	n/a	chr1:62207998-62208007 chr1:62207923-62207933
47	NFIC	chr1:62207691-62207933	HepG2	liver:	n/a	n/a
48	ELF1	chr1:62207703-62208456	GM12878	blood:	n/a	chr1:62208394-62208403
49	TEAD4	chr1:62207737-62208189	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr1:62207411-62208803	H1-neurons	neurons:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:62207888-62207938	CMK	blood:	n/a
2	chr1:62207888-62207938	Caco-2	colon:	n/a
3	chr1:62207888-62207938	HRPEpiC	eye:	n/a
4	chr1:62207888-62207938	AG09319	gingival:	n/a
5	chr1:62207888-62207938	AoSMC	blood vessel:	n/a
6	chr1:62207888-62207938	U87	brain:	n/a
7	chr1:62207888-62207938	HEK293	kidney:	embryo
8	chr1:62207888-62207938	NHDF-neo	bronchial:	n/a
9	chr1:62207888-62207938	HCF	heart:	n/a
10	chr1:62207888-62207938	H1-hESC	embryonic stem cell:	embryo
11	chr1:62207888-62207938	AG04449	skin:	fetal
12	chr1:62207888-62207938	BJ	skin:	n/a
13	chr1:62207888-62207938	ECC-1	luminal epithelium:	n/a
14	chr1:62207888-62207938	AG10803	skin:	n/a
15	chr1:62207888-62207938	SAEC	small airway:	n/a
16	chr1:62207888-62207938	NH-A	brain:	n/a
17	chr1:62207888-62207938	HCPEpiC	choroid plexus:	n/a
18	chr1:62207888-62207938	A549	lung:	n/a
19	chr1:62207888-62207938	Hepatocyte	liver:	n/a
20	chr1:62207888-62207938	GM06990	blood:	n/a
21	chr1:62207888-62207938	HUVEC	blood vessel:	n/a
22	chr1:62207888-62207938	PANC-1	pancreas:	n/a
23	chr1:62207888-62207938	NT2-D1	testis:	n/a
24	chr1:62207888-62207938	GM19239	blood:	n/a
25	chr1:62207888-62207938	NHBE	bronchial:	n/a
26	chr1:62207888-62207938	MCF-7	breast:	n/a
27	chr1:62207888-62207938	BE2_C	brain:	n/a
28	chr1:62207888-62207938	LNCaP	prostate:	n/a
29	chr1:62207888-62207938	HL-60	blood:	n/a
30	chr1:62207888-62207938	GM12878	blood:	n/a
31	chr1:62207888-62207938	HIPEpiC	eye:	n/a
32	chr1:62207888-62207938	GM12892	blood:	n/a
33	chr1:62207888-62207938	RPTEC	kidney:	n/a
34	chr1:62207888-62207938	AG04450	lung:	fetal
35	chr1:62207888-62207938	SK-N-SH	brain:	n/a
36	chr1:62207888-62207938	GM12891	blood:	n/a
37	chr1:62207888-62207938	PrEC	prostate:	n/a
38	chr1:62207888-62207938	HNPCEpiC	eye:	n/a
39	chr1:62207888-62207938	IMR90	lung:	fetal
40	chr1:62207888-62207938	HPAEpiC	pulmonary alveolar:	n/a
41	chr1:62207888-62207938	HepG2	liver:	n/a
42	chr1:62207888-62207938	HCM	heart:	n/a
43	chr1:62207888-62207938	HRCEpiC	kidney:	n/a
44	chr1:62207888-62207938	ovcar-3	ovarian:	n/a
45	chr1:62207888-62207938	SK-N-MC	brain:	n/a
46	chr1:62207888-62207938	AG09309	skin:	n/a
47	chr1:62207888-62207938	T-47D	breast:	n/a
48	chr1:62207888-62207938	PFSK-1	brain:	n/a
49	chr1:62207888-62207938	Jurkat	blood:	n/a
50	chr1:62207888-62207938	ProgFib	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:62207506..62208255-chr17:56708908..56709525,2	Hela-S3	cervix:
2	chr1:62190630..62191606-chr1:62207469..62208515,4	Hela-S3	cervix:
3	chr1:62207671..62208171-chr19:46271999..46272502,2	Hela-S3	cervix:
4	chr1:62173080..62176930-chr1:62205875..62209587,4	MCF-7	breast:
5	chr1:62188914..62195188-chr1:62202056..62212232,19	MCF-7	breast:
6	chr1:62207014..62208687-chr8:103424188..103425708,2	MCF-7	breast:
7	chr1:62207664..62208616-chr14:74318620..74319495,2	Hela-S3	cervix:
8	chr1:62187463..62192137-chr1:62206143..62210486,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TM2D1-4	chr1:62207670-62208096	ENSG00000271200.1

Variant related genes	Relation type
INADL	TF binding region
INADL	CpG island
ENSG00000258653	Chromatin interaction
ENSG00000140043	Chromatin interaction
ENSG00000162604	Chromatin interaction
ENSG00000104517	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000177045	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3422069	chr1:62206889-62209737	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	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	chr1:62206800-62208000	Bivalent/Poised TSS	HepG2	liver
2	chr1:62207000-62209800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:62207200-62208000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:62207200-62208000	Flanking Active TSS	Fetal Brain Male	brain
5	chr1:62207200-62208600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:62207200-62208600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:62207200-62208800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:62207200-62209000	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:62207200-62209000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:62207200-62209000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:62207200-62209000	Active TSS	Brain Angular Gyrus	brain
12	chr1:62207200-62209000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr1:62207200-62209000	Active TSS	Fetal Intestine Small	intestine
14	chr1:62207200-62209000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:62207200-62209000	Active TSS	NHDF-Ad	bronchial
16	chr1:62207200-62209200	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:62207200-62209200	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:62207200-62209200	Active TSS	Fetal Intestine Large	intestine
19	chr1:62207200-62209400	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:62207200-62209400	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr1:62207200-62209600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr1:62207200-62209600	Active TSS	H1 Cell Line	embryonic stem cell
23	chr1:62207200-62209600	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr1:62207200-62209600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr1:62207200-62209800	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr1:62207400-62208000	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr1:62207400-62208000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr1:62207400-62208000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr1:62207400-62208000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:62207400-62208000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:62207400-62208000	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr1:62207400-62208000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr1:62207400-62208400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
34	chr1:62207400-62208600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:62207400-62208600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:62207400-62208600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:62207400-62208600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:62207400-62208600	Active TSS	Fetal Muscle Trunk	muscle
39	chr1:62207400-62208600	Active TSS	Fetal Muscle Leg	muscle
40	chr1:62207400-62208800	Active TSS	Fetal Stomach	stomach
41	chr1:62207400-62209000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:62207400-62209000	Active TSS	Muscle Satellite Cultured Cells	--
43	chr1:62207400-62209000	Active TSS	Brain Cingulate Gyrus	brain
44	chr1:62207400-62209000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:62207400-62209000	Active TSS	Brain Substantia Nigra	brain
46	chr1:62207400-62209000	Active TSS	Colonic Mucosa	Colon
47	chr1:62207400-62209000	Active TSS	Pancreas	Pancrea
48	chr1:62207400-62209000	Bivalent/Poised TSS	Thymus	Thymus
49	chr1:62207400-62209000	Active TSS	NHLF	lung
50	chr1:62207400-62209000	Active TSS	Osteobl	bone

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