Variant report

Variant	rs3762262
Chromosome Location	chr1:153508875-153508876
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	MAX	chr1:153508194-153509136	SK-N-SH	brain:	n/a	chr1:153508744-153508753 chr1:153509055-153509062 chr1:153508744-153508753
2	MYC	chr1:153508441-153509075	HUVEC	blood vessel:	n/a	chr1:153508744-153508753 chr1:153509055-153509062 chr1:153508744-153508753
3	POLR2A	chr1:153504001-153509011	U87	brain:	n/a	n/a
4	GABPA	chr1:153508532-153508892	A549	lung:	n/a	n/a
5	POLR2A	chr1:153508111-153509537	ECC-1	luminal epithelium:	n/a	n/a
6	CTCF	chr1:153508760-153508910	HRE	kidney:	n/a	n/a
7	POLR2A	chr1:153508108-153508955	GM12878	blood:	n/a	n/a
8	USF2	chr1:153508587-153508911	H1-hESC	embryonic stem cell:	n/a	chr1:153508743-153508754
9	POLR2A	chr1:153505145-153509494	Hela-S3	cervix:	n/a	n/a
10	BHLHE40	chr1:153508583-153509002	K562	blood:	n/a	n/a
11	USF1	chr1:153508550-153508883	K562	blood:	n/a	chr1:153508743-153508754
12	SP1	chr1:153507532-153509311	A549	lung:	n/a	chr1:153507916-153507925 chr1:153507914-153507926 chr1:153507914-153507926 chr1:153509217-153509231 chr1:153509220-153509232 chr1:153508124-153508133 chr1:153507915-153507924 chr1:153508954-153508968 chr1:153507915-153507929
13	REST	chr1:153508533-153509298	A549	lung:	n/a	chr1:153509030-153509038
14	NRF1	chr1:153508016-153508987	SK-N-SH	brain:	n/a	n/a
15	NR3C1	chr1:153508373-153508951	A549	lung:	n/a	n/a
16	CREB1	chr1:153508206-153509028	A549	lung:	n/a	n/a
17	MAZ	chr1:153507790-153509028	GM12878	blood:	n/a	chr1:153508744-153508753 chr1:153508744-153508753
18	POLR2A	chr1:153507820-153508971	MCF10A-Er-Src	breast:	n/a	n/a
19	CTCF	chr1:153508860-153509010	HCPEpiC	choroid plexus:	n/a	n/a
20	BCL3	chr1:153507149-153509297	A549	lung:	n/a	n/a
21	POLR2A	chr1:153505307-153509454	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:153508364-153508881	GM12878	blood:	n/a	n/a
23	E2F6	chr1:153508544-153509220	A549	lung:	n/a	n/a
24	POLR2A	chr1:153508535-153509048	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:153505192-153509569	HCT-116	colon:	n/a	n/a
26	MAZ	chr1:153504643-153509324	IMR90	lung:	n/a	chr1:153506458-153506465 chr1:153508744-153508753 chr1:153506973-153506982 chr1:153509221-153509231 chr1:153506972-153506981 chr1:153509055-153509062 chr1:153508744-153508753
27	MAX	chr1:153505450-153509582	HCT-116	colon:	n/a	chr1:153506458-153506465 chr1:153508744-153508753 chr1:153506973-153506982 chr1:153509221-153509231 chr1:153506972-153506981 chr1:153509055-153509062 chr1:153508744-153508753
28	SMARCB1	chr1:153507275-153510073	Hela-S3	cervix:	n/a	n/a
29	ELF1	chr1:153508429-153508955	A549	lung:	n/a	n/a
30	EP300	chr1:153508508-153508938	T-47D	breast:	n/a	n/a
31	USF1	chr1:153508503-153509057	A549	lung:	n/a	chr1:153508743-153508754
32	TFAP2C	chr1:153507490-153509555	Hela-S3	cervix:	n/a	chr1:153508626-153508641
33	TBP	chr1:153507797-153509433	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr1:153508722-153508895	HepG2	liver:	n/a	n/a
35	MAX	chr1:153508137-153509225	SK-N-SH	brain:	n/a	chr1:153508744-153508753 chr1:153509055-153509062 chr1:153508744-153508753
36	FOXA2	chr1:153508362-153508947	A549	lung:	n/a	n/a
37	ELF1	chr1:153508171-153509110	A549	lung:	n/a	n/a
38	POLR2A	chr1:153507615-153509045	Gliobla	brain:	n/a	n/a
39	GATA3	chr1:153508480-153509009	T-47D	breast:	n/a	chr1:153508909-153508922 chr1:153508912-153508920
40	RFX5	chr1:153507637-153509011	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr1:153507471-153509361	A549	lung:	n/a	n/a
42	POLR2A	chr1:153507750-153509161	HL-60	blood:	n/a	n/a
43	MYC	chr1:153508533-153509402	MCF10A-Er-Src	breast:	n/a	chr1:153508744-153508753 chr1:153509221-153509231 chr1:153509055-153509062 chr1:153508744-153508753
44	USF1	chr1:153508566-153508902	K562	blood:	n/a	chr1:153508743-153508754
45	SIN3AK20	chr1:153507998-153508907	PANC-1	pancreas:	n/a	n/a
46	GATA3	chr1:153507980-153509170	A549	lung:	n/a	chr1:153508909-153508922 chr1:153508912-153508920
47	MAX	chr1:153507971-153509551	ECC-1	luminal epithelium:	n/a	chr1:153508744-153508753 chr1:153509221-153509231 chr1:153509055-153509062 chr1:153508744-153508753
48	FOS	chr1:153508594-153509016	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr1:153507967-153508945	GM12878	blood:	n/a	n/a
50	TFAP2A	chr1:153507731-153509541	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:153508860-153508910	AG09309	skin:	n/a
2	chr1:153508839-153508889	A549	lung:	n/a
3	chr1:153508839-153508889	PANC-1	pancreas:	n/a
4	chr1:153508839-153508889	GM12892	blood:	n/a
5	chr1:153508860-153508910	GM12892	blood:	n/a
6	chr1:153508875-153508925	K562	blood:	n/a
7	chr1:153508875-153508925	AG09309	skin:	n/a
8	chr1:153508860-153508910	HRE	kidney:	n/a
9	chr1:153508839-153508889	MCF10A-Er-Src	breast:	n/a
10	chr1:153508875-153508925	ECC-1	luminal epithelium:	n/a
11	chr1:153508860-153508910	BE2_C	brain:	n/a
12	chr1:153508875-153508925	NT2-D1	testis:	n/a
13	chr1:153508839-153508889	HCM	heart:	n/a
14	chr1:153508860-153508910	Jurkat	blood:	n/a
15	chr1:153508860-153508910	HNPCEpiC	eye:	n/a
16	chr1:153508875-153508925	HCPEpiC	choroid plexus:	n/a
17	chr1:153508839-153508889	PFSK-1	brain:	n/a
18	chr1:153508839-153508889	GM12891	blood:	n/a
19	chr1:153508875-153508925	U87	brain:	n/a
20	chr1:153508875-153508925	Caco-2	colon:	n/a
21	chr1:153508860-153508910	GM12891	blood:	n/a
22	chr1:153508839-153508889	T-47D	breast:	n/a
23	chr1:153508875-153508925	HNPCEpiC	eye:	n/a
24	chr1:153508839-153508889	H1-hESC	embryonic stem cell:	embryo
25	chr1:153508860-153508910	GM19239	blood:	n/a
26	chr1:153508860-153508910	HMEC	breast:	n/a
27	chr1:153508860-153508910	HCM	heart:	n/a
28	chr1:153508860-153508910	HEEpiC	esophagus:	n/a
29	chr1:153508860-153508910	NHDF-neo	bronchial:	n/a
30	chr1:153508875-153508925	SK-N-MC	brain:	n/a
31	chr1:153508860-153508910	PrEC	prostate:	n/a
32	chr1:153508860-153508910	HPAEpiC	pulmonary alveolar:	n/a
33	chr1:153508839-153508889	MCF-7	breast:	n/a
34	chr1:153508860-153508910	BJ	skin:	n/a
35	chr1:153508860-153508910	GM06990	blood:	n/a
36	chr1:153508875-153508925	AG10803	skin:	n/a
37	chr1:153508875-153508925	HAEpiC	amniotic membrane:	n/a
38	chr1:153508860-153508910	HIPEpiC	eye:	n/a
39	chr1:153508860-153508910	RPTEC	kidney:	n/a
40	chr1:153508860-153508910	SKMC	muscle:	n/a
41	chr1:153508875-153508925	HPAEpiC	pulmonary alveolar:	n/a
42	chr1:153508860-153508910	CMK	blood:	n/a
43	chr1:153508875-153508925	ProgFib	skin:	n/a
44	chr1:153508839-153508889	SKMC	muscle:	n/a
45	chr1:153508839-153508889	NB4	blood:	n/a
46	chr1:153508839-153508889	Jurkat	blood:	n/a
47	chr1:153508860-153508910	U87	brain:	n/a
48	chr1:153508860-153508910	HCT-116	colon:	n/a
49	chr1:153508839-153508889	NHBE	bronchial:	n/a
50	chr1:153508839-153508889	NH-A	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153508236..153509740-chr1:153522237..153524623,2	K562	blood:
2	chr1:153507285..153510261-chr1:153579792..153582160,3	MCF-7	breast:
3	chr1:153504925..153506891-chr1:153507588..153509186,2	K562	blood:
4	chr1:153507994..153509209-chr19:17622174..17622791,3	Hela-S3	cervix:
5	chr1:64058939..64059975-chr1:153508278..153509068,3	Hela-S3	cervix:
6	chr1:153506339..153510656-chr1:153517043..153519160,4	K562	blood:
7	chr1:153508696..153509209-chr12:52445108..52445670,2	Hela-S3	cervix:
8	chr1:153508215..153509143-chr4:100870830..100871549,2	Hela-S3	cervix:
9	chr1:153508043..153508984-chr15:83478155..83479111,2	Hela-S3	cervix:
10	chr1:153508402..153509226-chr12:21810151..21810795,2	Hela-S3	cervix:
11	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
12	chr1:153508212..153508984-chr1:201979397..201980003,2	Hela-S3	cervix:
13	chr1:153508634..153510673-chr1:153516202..153519160,2	K562	blood:
14	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
15	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
16	chr1:153508398..153508913-chr2:240323217..240323772,2	Hela-S3	cervix:
17	chr1:153508608..153510769-chr1:153600428..153603319,2	K562	blood:
18	chr1:153508391..153508964-chr17:62223072..62223763,2	Hela-S3	cervix:
19	chr1:153508326..153509270-chr7:73244870..73245787,2	Hela-S3	cervix:
20	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
21	chr1:153508630..153510790-chr1:153606132..153607908,2	K562	blood:
22	chr1:153508488..153510083-chr1:153537210..153538800,2	K562	blood:
23	chr1:153507230..153509062-chr1:153605925..153607769,2	MCF-7	breast:
24	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:
25	chr1:153508413..153509221-chr16:48418944..48419933,2	Hela-S3	cervix:
26	chr1:153508410..153508969-chr15:59225720..59226378,2	Hela-S3	cervix:
27	chr1:153508168..153508886-chr11:65266293..65266972,2	Hela-S3	cervix:

Variant related genes	Relation type
S100A6	TF binding region
S100A6	CpG island
ENSG00000189171	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000156232	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000111716	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000079739	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000269439	Chromatin interaction
ENSG00000163435	Chromatin interaction
ENSG00000137776	Chromatin interaction
ENSG00000266402	Chromatin interaction
ENSG00000130313	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000196470	Chromatin interaction
ENSG00000068024	Chromatin interaction
ENSG00000189143	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000222020	Chromatin interaction
ENSG00000234678	Chromatin interaction
ENSG00000142856	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs17695220	0.86[AMR][1000 genomes]
rs1887039	0.80[AMR][1000 genomes]
rs2094217	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094737	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094738	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2248745	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262587	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2339696	0.86[AMR][1000 genomes]
rs2480695	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480696	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427870	0.93[ASN][1000 genomes]
rs28464843	0.88[AMR][1000 genomes]
rs28483109	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4017737	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272569	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4430277	0.81[EUR][1000 genomes]
rs477339	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845351	0.83[EUR][1000 genomes]
rs4845352	0.84[EUR][1000 genomes]
rs4845555	0.80[AMR][1000 genomes]
rs532652	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs550597	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs552446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585215	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587743	0.86[AMR][1000 genomes]
rs659403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659755	0.86[AMR][1000 genomes]
rs6690638	0.80[AMR][1000 genomes]
rs6690712	0.80[AMR][1000 genomes]
rs7515940	0.81[AMR][1000 genomes]
rs7518306	0.83[EUR][1000 genomes]
rs7520093	0.88[AMR][1000 genomes]
rs7534343	0.88[AMR][1000 genomes]
rs7534347	0.88[AMR][1000 genomes]
rs7537898	0.81[AMR][1000 genomes]
rs7544359	0.81[AMR][1000 genomes]
rs9426945	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427239	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427287	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 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	chr1:153505800-153509200	Active TSS	Aorta	Aorta
2	chr1:153505800-153509400	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr1:153506800-153509000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr1:153506800-153509200	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr1:153507000-153509200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:153507000-153509400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:153507200-153509000	Flanking Active TSS	Spleen	Spleen
8	chr1:153507200-153509200	Flanking Active TSS	Fetal Muscle Trunk	muscle
9	chr1:153507400-153509400	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:153507400-153509600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:153507600-153509000	Active TSS	Fetal Kidney	kidney
12	chr1:153507600-153509000	Active TSS	Placenta Amnion	Placenta Amnion
13	chr1:153507600-153509000	Active TSS	Small Intestine	intestine
14	chr1:153507600-153509200	Flanking Active TSS	Fetal Thymus	thymus
15	chr1:153507600-153509400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr1:153507600-153509400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:153507600-153509400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:153507600-153509400	Flanking Active TSS	Esophagus	oesophagus
19	chr1:153507800-153509000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:153507800-153509000	Active TSS	Psoas Muscle	Psoas
21	chr1:153507800-153509000	Active TSS	Rectal Smooth Muscle	rectum
22	chr1:153507800-153509200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr1:153507800-153509200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:153507800-153509200	Active TSS	Ovary	ovary
25	chr1:153508000-153509000	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr1:153508000-153509000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
27	chr1:153508000-153509000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:153508000-153509000	Active TSS	Fetal Intestine Small	intestine
29	chr1:153508000-153509200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
30	chr1:153508200-153509000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr1:153508200-153509000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:153508200-153509000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr1:153508200-153509000	Active TSS	Brain Substantia Nigra	brain
34	chr1:153508200-153509000	Active TSS	Fetal Brain Female	brain
35	chr1:153508200-153509600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr1:153508400-153509000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr1:153508400-153509000	Active TSS	Brain Cingulate Gyrus	brain
38	chr1:153508400-153509000	Active TSS	Fetal Stomach	stomach
39	chr1:153508400-153509000	Active TSS	Right Atrium	heart
40	chr1:153508400-153509000	Active TSS	Right Ventricle	heart
41	chr1:153508400-153509200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:153508400-153509200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:153508600-153509000	Flanking Active TSS	Liver	Liver
44	chr1:153508600-153509000	Bivalent/Poised TSS	HepG2	liver
45	chr1:153508600-153509200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
46	chr1:153508600-153509200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:153508600-153509200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr1:153508600-153509200	Flanking Active TSS	Fetal Muscle Leg	muscle
49	chr1:153508600-153509200	Flanking Active TSS	Pancreas	Pancrea
50	chr1:153508600-153509200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle

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