Variant report

Variant	rs3738203
Chromosome Location	chr1:211556004-211556005
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	E2F6	chr1:211555690-211556626	K562	blood:	n/a	chr1:211556080-211556092 chr1:211555881-211555898 chr1:211555884-211555895 chr1:211555881-211555898 chr1:211555884-211555895 chr1:211556325-211556334 chr1:211555884-211555895 chr1:211555879-211555894 chr1:211556130-211556139 chr1:211555884-211555895 chr1:211555881-211555898
2	POLR2A	chr1:211555744-211556863	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:211555782-211556837	GM19193	blood:	n/a	n/a
4	HEY1	chr1:211555842-211556615	HepG2	liver:	n/a	n/a
5	E2F4	chr1:211555839-211556637	K562	blood:	n/a	chr1:211556080-211556092 chr1:211555881-211555898 chr1:211555884-211555895 chr1:211555881-211555898 chr1:211555884-211555895 chr1:211556325-211556334 chr1:211555884-211555895 chr1:211555879-211555894 chr1:211556130-211556139 chr1:211555884-211555895 chr1:211555881-211555898
6	EP300	chr1:211555137-211556915	GM12878	blood:	n/a	chr1:211555751-211555765
7	HDAC2	chr1:211555758-211556291	K562	blood:	n/a	chr1:211556131-211556140
8	MTA3	chr1:211555092-211557130	GM12878	blood:	n/a	n/a
9	SPI1	chr1:211555983-211556272	GM12891	blood:	n/a	n/a
10	TCF7L2	chr1:211555886-211556627	Hela-S3	cervix:	n/a	n/a
11	TAF1	chr1:211555999-211556755	Hela-S3	cervix:	n/a	n/a
12	CHD2	chr1:211555826-211556861	GM12878	blood:	n/a	n/a
13	E2F6	chr1:211555661-211556683	H1-hESC	embryonic stem cell:	n/a	chr1:211556080-211556092 chr1:211555881-211555898 chr1:211555884-211555895 chr1:211555881-211555898 chr1:211555884-211555895 chr1:211556325-211556334 chr1:211555884-211555895 chr1:211555879-211555894 chr1:211556130-211556139 chr1:211555884-211555895 chr1:211555881-211555898
14	TAF1	chr1:211555909-211556362	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr1:211555787-211556889	Hela-S3	cervix:	n/a	n/a
16	MAZ	chr1:211555296-211556886	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:211555767-211556613	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:211555749-211556962	K562	blood:	n/a	n/a
19	POLR2A	chr1:211555385-211557484	MCF10A-Er-Src	breast:	n/a	n/a
20	CEBPD	chr1:211555820-211556380	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:211555811-211556687	HepG2	liver:	n/a	n/a
22	EP300	chr1:211555171-211556608	K562	blood:	n/a	chr1:211555751-211555765
23	GABPA	chr1:211555830-211556800	MCF-7	breast:	n/a	chr1:211556573-211556580 chr1:211556129-211556140 chr1:211556131-211556140 chr1:211556129-211556143 chr1:211556126-211556140
24	TCF12	chr1:211555990-211556363	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:211555802-211556767	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr1:211555667-211556602	PFSK-1	brain:	n/a	n/a
27	EGR1	chr1:211555996-211556290	GM12878	blood:	n/a	chr1:211556063-211556072 chr1:211556131-211556140 chr1:211556130-211556139
28	ZKSCAN1	chr1:211555810-211556688	Hela-S3	cervix:	n/a	n/a
29	RFX5	chr1:211555980-211556659	HepG2	liver:	n/a	n/a
30	TAF1	chr1:211555791-211556537	ECC-1	luminal epithelium:	n/a	n/a
31	HDAC2	chr1:211555835-211556318	K562	blood:	n/a	chr1:211556131-211556140
32	STAT5A	chr1:211555658-211556788	K562	blood:	n/a	n/a
33	CEBPB	chr1:211555889-211556365	ECC-1	luminal epithelium:	n/a	n/a
34	NFIC	chr1:211555981-211556422	HepG2	liver:	n/a	n/a
35	CEBPB	chr1:211555895-211556287	A549	lung:	n/a	n/a
36	TEAD4	chr1:211555526-211557063	K562	blood:	n/a	n/a
37	RAD21	chr1:211555927-211556342	SK-N-SH_RA	brain:	n/a	n/a
38	POLR2A	chr1:211555782-211556629	A549	lung:	n/a	n/a
39	ATF2	chr1:211555948-211556411	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:211555701-211556890	Hela-S3	cervix:	n/a	n/a
41	TCF12	chr1:211555688-211556853	A549	lung:	n/a	n/a
42	REST	chr1:211555682-211556907	A549	lung:	n/a	n/a
43	HA-E2F1	chr1:211555923-211556354	Hela-S3	cervix:	n/a	chr1:211556080-211556092 chr1:211556325-211556334 chr1:211556130-211556139
44	ELF1	chr1:211555812-211556735	GM12878	blood:	n/a	n/a
45	MYC	chr1:211555408-211556744	K562	blood:	n/a	n/a
46	TBL1XR1	chr1:211555777-211556849	K562	blood:	n/a	n/a
47	POU2F2	chr1:211555878-211556551	GM12891	blood:	n/a	n/a
48	POLR2A	chr1:211555706-211556799	HCT-116	colon:	n/a	n/a
49	POLR2A	chr1:211555737-211556694	A549	lung:	n/a	n/a
50	ZBTB33	chr1:211555969-211556294	A549	lung:	n/a	chr1:211556054-211556064

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:211555968-211556018	BJ	skin:	n/a
2	chr1:211555983-211556033	SK-N-SH_RA	brain:	n/a
3	chr1:211555998-211556048	Hela-S3	cervix:	n/a
4	chr1:211555983-211556033	K562	blood:	n/a
5	chr1:211555998-211556048	HPAEpiC	pulmonary alveolar:	n/a
6	chr1:211555998-211556048	AoSMC	blood vessel:	n/a
7	chr1:211555998-211556048	GM06990	blood:	n/a
8	chr1:211555983-211556033	HEEpiC	esophagus:	n/a
9	chr1:211555998-211556048	T-47D	breast:	n/a
10	chr1:211555968-211556018	HRCEpiC	kidney:	n/a
11	chr1:211555968-211556018	AG04449	skin:	fetal
12	chr1:211555968-211556018	Caco-2	colon:	n/a
13	chr1:211555968-211556018	AG09319	gingival:	n/a
14	chr1:211555983-211556033	GM06990	blood:	n/a
15	chr1:211555983-211556033	H1-hESC	embryonic stem cell:	embryo
16	chr1:211555983-211556033	PANC-1	pancreas:	n/a
17	chr1:211555983-211556033	HepG2	liver:	n/a
18	chr1:211555998-211556048	A549	lung:	n/a
19	chr1:211555968-211556018	SK-N-SH	brain:	n/a
20	chr1:211555998-211556048	NT2-D1	testis:	n/a
21	chr1:211555998-211556048	HCPEpiC	choroid plexus:	n/a
22	chr1:211555968-211556018	GM12891	blood:	n/a
23	chr1:211555998-211556048	ProgFib	skin:	n/a
24	chr1:211555983-211556033	RPTEC	kidney:	n/a
25	chr1:211555968-211556018	NB4	blood:	n/a
26	chr1:211555983-211556033	HIPEpiC	eye:	n/a
27	chr1:211555998-211556048	GM12892	blood:	n/a
28	chr1:211555968-211556018	HUVEC	blood vessel:	n/a
29	chr1:211555998-211556048	GM12878	blood:	n/a
30	chr1:211555998-211556048	SAEC	small airway:	n/a
31	chr1:211555968-211556018	HMEC	breast:	n/a
32	chr1:211555968-211556018	GM12878	blood:	n/a
33	chr1:211555998-211556048	PANC-1	pancreas:	n/a
34	chr1:211555983-211556033	HL-60	blood:	n/a
35	chr1:211555998-211556048	MCF-7	breast:	n/a
36	chr1:211555983-211556033	AoSMC	blood vessel:	n/a
37	chr1:211555998-211556048	HCM	heart:	n/a
38	chr1:211555968-211556018	A549	lung:	n/a
39	chr1:211555998-211556048	Jurkat	blood:	n/a
40	chr1:211555983-211556033	HPAEpiC	pulmonary alveolar:	n/a
41	chr1:211555968-211556018	AoSMC	blood vessel:	n/a
42	chr1:211555998-211556048	CMK	blood:	n/a
43	chr1:211555983-211556033	NB4	blood:	n/a
44	chr1:211555968-211556018	T-47D	breast:	n/a
45	chr1:211555998-211556048	ECC-1	luminal epithelium:	n/a
46	chr1:211555983-211556033	SAEC	small airway:	n/a
47	chr1:211555968-211556018	HEEpiC	esophagus:	n/a
48	chr1:211555968-211556018	NHDF-neo	bronchial:	n/a
49	chr1:211555998-211556048	HepG2	liver:	n/a
50	chr1:211555983-211556033	ProgFib	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:211555242..211556502-chr12:52444709..52445693,3	Hela-S3	cervix:
2	chr1:211499136..211502907-chr1:211554932..211557555,4	K562	blood:
3	chr1:211555901..211556720-chr8:37962753..37963521,2	Hela-S3	cervix:
4	chr1:211555896..211556746-chr15:23034284..23034846,2	Hela-S3	cervix:
5	chr1:211555829..211556746-chr9:127631369..127631980,2	Hela-S3	cervix:
6	chr1:211555733..211556481-chr12:53341701..53342658,2	Hela-S3	cervix:
7	chr1:211555799..211556573-chr12:49075458..49076102,2	Hela-S3	cervix:
8	chr1:211430859..211434419-chr1:211555069..211558654,5	K562	blood:
9	chr1:211555563..211556502-chr2:85132519..85133250,2	Hela-S3	cervix:
10	chr1:211555727..211556435-chr6:4018361..4019306,2	Hela-S3	cervix:
11	chr1:211555944..211556496-chr4:77996087..77996921,2	HCT-116	colon:
12	chr1:211555959..211556660-chr19:49652554..49653253,2	Hela-S3	cervix:
13	chr1:17765809..17766729-chr1:211555793..211556618,2	Hela-S3	cervix:
14	chr1:211555498..211556396-chr6:30584300..30585176,2	Hela-S3	cervix:
15	chr1:211540485..211542540-chr1:211554956..211557564,2	K562	blood:
16	chr1:211555281..211556191-chr14:23775905..23776674,2	Hela-S3	cervix:
17	chr1:76251857..76252383-chr1:211555859..211556371,2	Hela-S3	cervix:

Variant related genes	Relation type
LINC00467	TF binding region
LINC00467	CpG island
ENSG00000139620	Chromatin interaction
ENSG00000136950	Chromatin interaction
ENSG00000272248	Chromatin interaction
ENSG00000117625	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000129691	Chromatin interaction
ENSG00000118816	Chromatin interaction
ENSG00000179051	Chromatin interaction
ENSG00000034510	Chromatin interaction
ENSG00000111057	Chromatin interaction
ENSG00000140157	Chromatin interaction
ENSG00000129473	Chromatin interaction
ENSG00000258643	Chromatin interaction
ENSG00000177380	Chromatin interaction
ENSG00000082512	Chromatin interaction
ENSG00000137955	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17017431	0.82[AFR][1000 genomes]
rs17017432	0.82[AFR][1000 genomes]
rs17017441	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17017451	0.83[AFR][1000 genomes]
rs34318448	0.81[AFR][1000 genomes]
rs61848982	0.81[AFR][1000 genomes]
rs6699139	0.81[AFR][1000 genomes]
rs7529673	0.88[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762141	chr1:211538685-211603843	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211555000-211556600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:211555000-211557000	Active TSS	Psoas Muscle	Psoas
3	chr1:211555000-211557400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr1:211555200-211556400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:211555200-211556400	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr1:211555200-211556600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:211555200-211556600	Active TSS	Brain Anterior Caudate	brain
8	chr1:211555200-211556600	Active TSS	NHEK	skin
9	chr1:211555200-211556800	Active TSS	Duodenum Mucosa	Duodenum
10	chr1:211555200-211557200	Active TSS	K562	blood
11	chr1:211555400-211556200	Active TSS	Brain Germinal Matrix	brain
12	chr1:211555400-211556400	Active TSS	Primary T cells from cord blood	blood
13	chr1:211555400-211556600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:211555400-211556600	Active TSS	Liver	Liver
15	chr1:211555400-211556600	Active TSS	Brain Substantia Nigra	brain
16	chr1:211555400-211556600	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr1:211555400-211556600	Active TSS	Rectal Smooth Muscle	rectum
18	chr1:211555400-211556600	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr1:211555400-211556600	Active TSS	Stomach Mucosa	stomach
20	chr1:211555400-211556600	Active TSS	NHLF	lung
21	chr1:211555400-211556600	Active TSS	Osteobl	bone
22	chr1:211555400-211556800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:211555400-211556800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:211555400-211556800	Active TSS	Aorta	Aorta
25	chr1:211555400-211556800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:211555400-211556800	Active TSS	Fetal Kidney	kidney
27	chr1:211555400-211556800	Active TSS	Fetal Lung	lung
28	chr1:211555400-211556800	Active TSS	Fetal Stomach	stomach
29	chr1:211555400-211557000	Active TSS	H1 Cell Line	embryonic stem cell
30	chr1:211555400-211557000	Active TSS	Fetal Brain Female	brain
31	chr1:211555400-211557000	Active TSS	Fetal Muscle Leg	muscle
32	chr1:211555400-211557000	Active TSS	Right Ventricle	heart
33	chr1:211555400-211557200	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr1:211555400-211557200	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:211555600-211556400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:211555600-211556400	Active TSS	Primary T cells fromperipheralblood	blood
37	chr1:211555600-211556400	Active TSS	Placenta	Placenta
38	chr1:211555600-211556600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:211555600-211556600	Active TSS	Brain Angular Gyrus	brain
40	chr1:211555600-211556600	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr1:211555600-211556600	Active TSS	Thymus	Thymus
42	chr1:211555600-211556600	Active TSS	Hela-S3	cervix
43	chr1:211555600-211556600	Active TSS	HMEC	breast
44	chr1:211555600-211556600	Active TSS	HSMMtube	muscle
45	chr1:211555600-211556800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr1:211555600-211556800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:211555600-211556800	Active TSS	Colonic Mucosa	Colon
48	chr1:211555600-211556800	Active TSS	Fetal Intestine Large	intestine
49	chr1:211555600-211556800	Active TSS	Fetal Intestine Small	intestine
50	chr1:211555600-211556800	Active TSS	Stomach Smooth Muscle	stomach

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