Variant report

Variant	rs533952193
Chromosome Location	chr1:62208031-62208032
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	chr1:62207928-62208829	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:62207659-62208330	H1-hESC	embryonic stem cell:	n/a	n/a
3	NFIC	chr1:62207701-62208376	ECC-1	luminal epithelium:	n/a	n/a
4	MAZ	chr1:62207907-62208368	HepG2	liver:	n/a	chr1:62207998-62208007 chr1:62207923-62207933
5	POLR2A	chr1:62207653-62209116	MCF-7	breast:	n/a	n/a
6	POLR2A	chr1:62207784-62208052	A549	lung:	n/a	n/a
7	ESR1	chr1:62207753-62208276	T-47D	breast:	n/a	n/a
8	TEAD4	chr1:62207769-62208189	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:62207698-62209183	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:62207807-62208194	Raji	blood:	n/a	n/a
11	POLR2A	chr1:62207121-62209260	Hela-S3	cervix:	n/a	n/a
12	PML	chr1:62207922-62208433	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr1:62207525-62208538	MCF-7	breast:	n/a	n/a
14	POLR2A	chr1:62207185-62209561	MCF10A-Er-Src	breast:	n/a	n/a
15	GATA3	chr1:62207580-62208110	MCF-7	breast:	n/a	chr1:62207735-62207745
16	REST	chr1:62207435-62208882	H1-neurons	neurons:	n/a	chr1:62208295-62208308
17	JUND	chr1:62207668-62208368	H1-hESC	embryonic stem cell:	n/a	chr1:62208351-62208360 chr1:62208355-62208364
18	TAF7	chr1:62207905-62208382	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:62207795-62208819	GM18526	blood:	n/a	n/a
20	POLR2A	chr1:62208019-62208292	HepG2	liver:	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	GABPA	chr1:62208024-62208259	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:62207736-62208671	GM12892	blood:	n/a	n/a
27	MYC	chr1:62207936-62208750	MCF10A-Er-Src	breast:	n/a	chr1:62207998-62208007
28	TCF3	chr1:62207982-62208365	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:62207733-62208921	GM19193	blood:	n/a	n/a
30	ZEB1	chr1:62207712-62208619	GM12878	blood:	n/a	chr1:62208160-62208169 chr1:62208121-62208130 chr1:62208122-62208129 chr1:62207978-62207989
31	YY1	chr1:62207722-62208340	HCT-116	colon:	n/a	chr1:62207922-62207931
32	POLR2A	chr1:62207983-62208792	HepG2	liver:	n/a	n/a
33	ZNF263	chr1:62207363-62209211	HEK293-T-REx	kidney:	n/a	n/a
34	POLR2A	chr1:62207907-62208884	ProgFib	skin:	n/a	n/a
35	POLR2A	chr1:62207833-62208859	A549	lung:	n/a	n/a
36	MAX	chr1:62207620-62208818	ECC-1	luminal epithelium:	n/a	chr1:62207998-62208007 chr1:62207923-62207933 chr1:62207695-62207704
37	MAX	chr1:62207415-62209080	Hela-S3	cervix:	n/a	chr1:62207998-62208007 chr1:62207923-62207933 chr1:62207582-62207591 chr1:62207695-62207704
38	POLR2A	chr1:62207745-62208919	GM18951	blood:	n/a	n/a
39	POLR2A	chr1:62207388-62209264	Hela-S3	cervix:	n/a	n/a
40	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
41	MAX	chr1:62207639-62209010	HepG2	liver:	n/a	chr1:62207998-62208007 chr1:62207923-62207933 chr1:62207695-62207704
42	GATA3	chr1:62207684-62208307	T-47D	breast:	n/a	chr1:62207735-62207745
43	ELF1	chr1:62207905-62208326	HepG2	liver:	n/a	n/a
44	CHD2	chr1:62207792-62209002	GM12878	blood:	n/a	chr1:62208102-62208112 chr1:62208348-62208358 chr1:62207920-62207930
45	TAF1	chr1:62207763-62208106	MCF-7	breast:	n/a	n/a
46	YY1	chr1:62207716-62208322	ECC-1	luminal epithelium:	n/a	chr1:62207922-62207931
47	POLR2A	chr1:62207718-62209059	HepG2	liver:	n/a	n/a
48	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
49	MAX	chr1:62207773-62208397	H1-hESC	embryonic stem cell:	n/a	chr1:62207998-62208007 chr1:62207923-62207933
50	ZBTB7A	chr1:62208005-62209031	ECC-1	luminal epithelium:	n/a	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
ENSG00000258653	Chromatin interaction
ENSG00000162604	Chromatin interaction
ENSG00000177045	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000104517	Chromatin interaction
ENSG00000140043	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	chr1:62207000-62209800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:62207200-62208600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:62207200-62208600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:62207200-62208800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:62207200-62209000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:62207200-62209000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:62207200-62209000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:62207200-62209000	Active TSS	Brain Angular Gyrus	brain
9	chr1:62207200-62209000	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr1:62207200-62209000	Active TSS	Fetal Intestine Small	intestine
11	chr1:62207200-62209000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr1:62207200-62209000	Active TSS	NHDF-Ad	bronchial
13	chr1:62207200-62209200	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:62207200-62209200	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr1:62207200-62209200	Active TSS	Fetal Intestine Large	intestine
16	chr1:62207200-62209400	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr1:62207200-62209400	Active TSS	Sigmoid Colon	Sigmoid Colon
18	chr1:62207200-62209600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr1:62207200-62209600	Active TSS	H1 Cell Line	embryonic stem cell
20	chr1:62207200-62209600	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr1:62207200-62209600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:62207200-62209800	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr1:62207400-62208400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
24	chr1:62207400-62208600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:62207400-62208600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:62207400-62208600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:62207400-62208600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:62207400-62208600	Active TSS	Fetal Muscle Trunk	muscle
29	chr1:62207400-62208600	Active TSS	Fetal Muscle Leg	muscle
30	chr1:62207400-62208800	Active TSS	Fetal Stomach	stomach
31	chr1:62207400-62209000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:62207400-62209000	Active TSS	Muscle Satellite Cultured Cells	--
33	chr1:62207400-62209000	Active TSS	Brain Cingulate Gyrus	brain
34	chr1:62207400-62209000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:62207400-62209000	Active TSS	Brain Substantia Nigra	brain
36	chr1:62207400-62209000	Active TSS	Colonic Mucosa	Colon
37	chr1:62207400-62209000	Active TSS	Pancreas	Pancrea
38	chr1:62207400-62209000	Bivalent/Poised TSS	Thymus	Thymus
39	chr1:62207400-62209000	Active TSS	NHLF	lung
40	chr1:62207400-62209000	Active TSS	Osteobl	bone
41	chr1:62207400-62209200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:62207400-62209200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:62207400-62209400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:62207400-62209400	Active TSS	Esophagus	oesophagus
45	chr1:62207400-62209400	Active TSS	Ovary	ovary
46	chr1:62207400-62209400	Active TSS	Stomach Smooth Muscle	stomach
47	chr1:62207400-62209600	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr1:62207400-62209600	Active TSS	Aorta	Aorta
49	chr1:62207400-62209800	Active TSS	H9 Cell Line	embryonic stem cell
50	chr1:62207600-62208200	Flanking Active TSS	Primary B cells from cord blood	blood

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