Variant report

Variant	rs1532485
Chromosome Location	chr3:180319981-180319982
allele	G/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	GATA3	chr3:180319499-180320338	A549	lung:	n/a	n/a
2	CEBPB	chr3:180319878-180321043	A549	lung:	n/a	chr3:180320374-180320383 chr3:180320373-180320384 chr3:180320372-180320385 chr3:180320372-180320383
3	TCF7L2	chr3:180319591-180320508	Hela-S3	cervix:	n/a	n/a
4	HEY1	chr3:180319470-180320552	HepG2	liver:	n/a	chr3:180319875-180319890
5	HEY1	chr3:180319566-180320232	K562	blood:	n/a	chr3:180319875-180319890
6	POLR2A	chr3:180319084-180320647	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:180319357-180320575	GM19193	blood:	n/a	n/a
8	NFYB	chr3:180319588-180320053	Hela-S3	cervix:	n/a	n/a
9	TBP	chr3:180319644-180320751	Hela-S3	cervix:	n/a	n/a
10	BACH1	chr3:180319671-180320394	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:180319592-180320500	Hela-S3	cervix:	n/a	n/a
12	CHD1	chr3:180319412-180320233	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:180319339-180320262	HCT-116	colon:	n/a	n/a
14	ETS1	chr3:180319724-180320277	K562	blood:	n/a	chr3:180319899-180319910 chr3:180319901-180319910 chr3:180319763-180319777 chr3:180319901-180319910 chr3:180319934-180319943 chr3:180319765-180319776 chr3:180319934-180319943 chr3:180319961-180319972 chr3:180319933-180319946 chr3:180319934-180319943 chr3:180319932-180319942 chr3:180319934-180319943 chr3:180319962-180319973 chr3:180319931-180319947 chr3:180319934-180319943
15	FOXA2	chr3:180319657-180320089	HepG2	liver:	n/a	n/a
16	HA-E2F1	chr3:180319475-180320637	MCF-7	breast:	n/a	chr3:180319873-180319882
17	POLR2A	chr3:180319601-180320166	HepG2	liver:	n/a	n/a
18	MAX	chr3:180319591-180320391	Hela-S3	cervix:	n/a	chr3:180320353-180320363
19	SPI1	chr3:180319793-180320406	GM12891	blood:	n/a	chr3:180320293-180320300
20	TAF1	chr3:180319470-180320052	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:180319071-180320409	HEK293	kidney:	n/a	n/a
22	ZBTB33	chr3:180319379-180320403	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr3:180319099-180320508	K562	blood:	n/a	n/a
24	POLR2A	chr3:180319471-180320224	HUVEC	blood vessel:	n/a	n/a
25	TBP	chr3:180319396-180320532	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr3:180319126-180320489	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:180319521-180320472	GM12878	blood:	n/a	n/a
28	ZBTB33	chr3:180319535-180320103	GM12878	blood:	n/a	n/a
29	CREB1	chr3:180319479-180320282	H1-hESC	embryonic stem cell:	n/a	n/a
30	ELK4	chr3:180319611-180320435	Hela-S3	cervix:	n/a	chr3:180319899-180319910 chr3:180319932-180319943
31	MAZ	chr3:180319247-180320552	Hela-S3	cervix:	n/a	chr3:180320353-180320363
32	IRF4	chr3:180319639-180320221	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:180319250-180320511	Hela-S3	cervix:	n/a	n/a
34	REST	chr3:180319515-180320643	HL-60	blood:	n/a	n/a
35	POLR2A	chr3:180319607-180320430	HepG2	liver:	n/a	n/a
36	SIN3AK20	chr3:180319650-180320451	PANC-1	pancreas:	n/a	n/a
37	CHD2	chr3:180319484-180320428	Hela-S3	cervix:	n/a	n/a
38	ZBTB33	chr3:180319599-180320059	HepG2	liver:	n/a	n/a
39	MAX	chr3:180319504-180320363	K562	blood:	n/a	chr3:180320353-180320363
40	CTCFL	chr3:180319794-180319988	K562	blood:	n/a	n/a
41	TAL1	chr3:180319224-180320145	K562	blood:	n/a	n/a
42	GABPA	chr3:180319564-180320514	K562	blood:	n/a	chr3:180319961-180319968
43	CTCF	chr3:180319900-180320050	BJ	skin:	n/a	n/a
44	MAX	chr3:180319376-180319997	H1-hESC	embryonic stem cell:	n/a	n/a
45	NFIC	chr3:180319578-180320473	GM12878	blood:	n/a	n/a
46	TCF7L2	chr3:180319479-180320217	PANC-1	pancreas:	n/a	n/a
47	REST	chr3:180319639-180320118	A549	lung:	n/a	n/a
48	GABPA	chr3:180319158-180320827	MCF-7	breast:	n/a	chr3:180319961-180319968
49	ELK1	chr3:180319539-180320407	GM12878	blood:	n/a	chr3:180319934-180319943 chr3:180319934-180319943
50	TCF12	chr3:180319856-180320117	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:180319964-180320014	SAEC	small airway:	n/a
2	chr3:180319964-180320014	BE2_C	brain:	n/a
3	chr3:180319964-180320014	HAEpiC	amniotic membrane:	n/a
4	chr3:180319964-180320014	HCF	heart:	n/a
5	chr3:180319964-180320014	PrEC	prostate:	n/a
6	chr3:180319964-180320014	MCF-7	breast:	n/a
7	chr3:180319964-180320014	HCM	heart:	n/a
8	chr3:180319964-180320014	HNPCEpiC	eye:	n/a
9	chr3:180319964-180320014	AG10803	skin:	n/a
10	chr3:180319964-180320014	AG04449	skin:	fetal
11	chr3:180319964-180320014	IMR90	lung:	fetal
12	chr3:180319964-180320014	NT2-D1	testis:	n/a
13	chr3:180319964-180320014	RPTEC	kidney:	n/a
14	chr3:180319964-180320014	NHDF-neo	bronchial:	n/a
15	chr3:180319964-180320014	HEK293	kidney:	embryo
16	chr3:180319964-180320014	ProgFib	skin:	n/a
17	chr3:180319964-180320014	HPAEpiC	pulmonary alveolar:	n/a
18	chr3:180319964-180320014	ECC-1	luminal epithelium:	n/a
19	chr3:180319964-180320014	H1-hESC	embryonic stem cell:	embryo
20	chr3:180319964-180320014	HMEC	breast:	n/a
21	chr3:180319964-180320014	PANC-1	pancreas:	n/a
22	chr3:180319964-180320014	Caco-2	colon:	n/a
23	chr3:180319964-180320014	GM12891	blood:	n/a
24	chr3:180319964-180320014	CMK	blood:	n/a
25	chr3:180319964-180320014	HRE	kidney:	n/a
26	chr3:180319964-180320014	AoSMC	blood vessel:	n/a
27	chr3:180319964-180320014	MCF10A-Er-Src	breast:	n/a
28	chr3:180319964-180320014	SK-N-MC	brain:	n/a
29	chr3:180319964-180320014	HepG2	liver:	n/a
30	chr3:180319964-180320014	HUVEC	blood vessel:	n/a
31	chr3:180319964-180320014	AG09319	gingival:	n/a
32	chr3:180319964-180320014	NH-A	brain:	n/a
33	chr3:180319964-180320014	HEEpiC	esophagus:	n/a
34	chr3:180319964-180320014	AG09309	skin:	n/a
35	chr3:180319964-180320014	A549	lung:	n/a
36	chr3:180319964-180320014	GM19239	blood:	n/a
37	chr3:180319964-180320014	T-47D	breast:	n/a
38	chr3:180319964-180320014	NHBE	bronchial:	n/a
39	chr3:180319964-180320014	U87	brain:	n/a
40	chr3:180319964-180320014	GM06990	blood:	n/a
41	chr3:180319964-180320014	HCT-116	colon:	n/a
42	chr3:180319964-180320014	HRCEpiC	kidney:	n/a
43	chr3:180319964-180320014	Jurkat	blood:	n/a
44	chr3:180319964-180320014	HL-60	blood:	n/a
45	chr3:180319964-180320014	Hepatocyte	liver:	n/a
46	chr3:180319964-180320014	SKMC	muscle:	n/a
47	chr3:180319964-180320014	AG04450	lung:	fetal
48	chr3:180319964-180320014	BJ	skin:	n/a
49	chr3:180319964-180320014	K562	blood:	n/a
50	chr3:180319964-180320014	GM12878	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:180306061..180309253-chr3:180317592..180321304,5	K562	blood:
2	chr1:6761358..6761964-chr3:180319687..180320358,2	Hela-S3	cervix:
3	chr10:60144608..60145556-chr3:180319926..180320547,2	Hela-S3	cervix:
4	chr2:47596130..47596899-chr3:180319390..180320186,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000239774	TF binding region
TTC14	TF binding region
ENSG00000239774	CpG island
TTC14	CpG island
ENSG00000119888	Chromatin interaction
ENSG00000241946	Chromatin interaction
ENSG00000007923	Chromatin interaction
ENSG00000108064	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1353679	0.93[EUR][1000 genomes]
rs1603658	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17707963	0.85[EUR][1000 genomes]
rs17708913	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17764356	1.00[CEU][hapmap]
rs28385473	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28495789	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62291004	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62291005	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62291006	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62291007	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62291008	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62291009	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62291043	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62291045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62291048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6770664	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6774942	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9290705	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9819839	0.86[EUR][1000 genomes]
rs9837678	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9846858	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9847201	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9857489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9858483	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9864959	0.86[EUR][1000 genomes]
rs9865590	0.80[YRI][hapmap]
rs9866580	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9872076	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9876153	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9877497	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	nsv1007831	chr3:180162003-180348203	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536818	chr3:180162003-180348203	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3359190	chr3:180298396-180397223	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1532485	LAMP3	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180318800-180320200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:180318800-180321000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:180318800-180321200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:180319000-180320000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:180319000-180320600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:180319000-180320800	Active TSS	Brain Cingulate Gyrus	brain
7	chr3:180319000-180320800	Active TSS	Brain Substantia Nigra	brain
8	chr3:180319000-180321000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr3:180319000-180321000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr3:180319000-180321000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:180319000-180321000	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr3:180319000-180321000	Active TSS	NH-A	brain
13	chr3:180319000-180321200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr3:180319000-180321200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:180319000-180321400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr3:180319000-180321400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:180319000-180321400	Active TSS	GM12878-XiMat	blood
18	chr3:180319200-180320200	Active TSS	Primary hematopoietic stem cells	blood
19	chr3:180319200-180320400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
20	chr3:180319200-180320600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr3:180319200-180320600	Active TSS	Brain Anterior Caudate	brain
22	chr3:180319200-180320600	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr3:180319200-180320600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr3:180319200-180320600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr3:180319200-180320800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:180319200-180320800	Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr3:180319200-180320800	Active TSS	Brain Hippocampus Middle	brain
28	chr3:180319200-180320800	Active TSS	Colon Smooth Muscle	Colon
29	chr3:180319200-180320800	Active TSS	Placenta Amnion	Placenta Amnion
30	chr3:180319200-180320800	Active TSS	Stomach Smooth Muscle	stomach
31	chr3:180319200-180320800	Active TSS	HSMM	muscle
32	chr3:180319200-180321000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:180319200-180321000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:180319200-180321000	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr3:180319200-180321000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:180319200-180321000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr3:180319200-180321000	Active TSS	Primary T cells fromperipheralblood	blood
38	chr3:180319200-180321000	Active TSS	Colonic Mucosa	Colon
39	chr3:180319200-180321000	Active TSS	Fetal Intestine Large	intestine
40	chr3:180319200-180321000	Active TSS	Placenta	Placenta
41	chr3:180319200-180321000	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr3:180319200-180321200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:180319200-180321200	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr3:180319200-180321200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:180319200-180321200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:180319200-180321200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:180319200-180321200	Active TSS	Rectal Smooth Muscle	rectum
48	chr3:180319200-180321200	Active TSS	Right Atrium	heart
49	chr3:180319200-180321200	Active TSS	HSMMtube	muscle
50	chr3:180319200-180321200	Active TSS	NHLF	lung

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