Variant report

Variant	rs3813638
Chromosome Location	chr1:178994644-178994645
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	SP1	chr1:178994557-178995081	H1-hESC	embryonic stem cell:	n/a	chr1:178995014-178995026 chr1:178995015-178995024 chr1:178995027-178995037 chr1:178994727-178994741
2	TBP	chr1:178994554-178995946	H1-hESC	embryonic stem cell:	n/a	n/a
3	EP300	chr1:178994637-178995165	A549	lung:	n/a	chr1:178994709-178994723 chr1:178994838-178994847 chr1:178994834-178994843
4	EGR1	chr1:178994406-178996036	HCT-116	colon:	n/a	chr1:178995078-178995091 chr1:178995015-178995025 chr1:178995104-178995118 chr1:178994836-178994845 chr1:178995018-178995031
5	POLR2A	chr1:178994316-178996287	K562	blood:	n/a	n/a
6	YY1	chr1:178994380-178995080	H1-hESC	embryonic stem cell:	n/a	chr1:178994812-178994826 chr1:178995018-178995027 chr1:178994908-178994922 chr1:178994812-178994821
7	POLR2A	chr1:178994560-178996030	K562	blood:	n/a	n/a
8	RFX5	chr1:178994631-178996250	Hela-S3	cervix:	n/a	n/a
9	TAF7	chr1:178994471-178995023	H1-hESC	embryonic stem cell:	n/a	n/a
10	SMARCB1	chr1:178994232-178995968	Hela-S3	cervix:	n/a	n/a
11	EGR1	chr1:178994600-178995495	H1-hESC	embryonic stem cell:	n/a	chr1:178995078-178995091 chr1:178995015-178995025 chr1:178995104-178995118 chr1:178994836-178994845 chr1:178995018-178995031
12	MAZ	chr1:178994405-178996650	IMR90	lung:	n/a	chr1:178995016-178995026
13	MAX	chr1:178994467-178996244	A549	lung:	n/a	chr1:178995016-178995026
14	ETS1	chr1:178994519-178995914	K562	blood:	n/a	chr1:178995016-178995027 chr1:178995720-178995731
15	RAD21	chr1:178994557-178995007	H1-hESC	embryonic stem cell:	n/a	n/a
16	GATA3	chr1:178994576-178996254	A549	lung:	n/a	chr1:178994769-178994779 chr1:178994704-178994714 chr1:178995963-178995980 chr1:178995969-178995985
17	TEAD4	chr1:178994358-178996645	K562	blood:	n/a	chr1:178996267-178996276
18	ELK1	chr1:178994561-178995081	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:178994470-178995115	SK-N-MC	brain:	n/a	n/a
20	CTCF	chr1:178994560-178994710	A549	lung:	n/a	n/a
21	CTCF	chr1:178994407-178994989	K562	blood:	n/a	chr1:178994908-178994921
22	MAX	chr1:178994590-178995125	H1-hESC	embryonic stem cell:	n/a	chr1:178995016-178995026
23	POLR2A	chr1:178994029-178996204	K562	blood:	n/a	n/a
24	POLR2A	chr1:178994327-178996348	Hela-S3	cervix:	n/a	n/a
25	TCF12	chr1:178994213-178995132	A549	lung:	n/a	n/a
26	SP1	chr1:178994448-178995613	A549	lung:	n/a	chr1:178995014-178995026 chr1:178995311-178995320 chr1:178995082-178995093 chr1:178995015-178995024 chr1:178995027-178995037 chr1:178994727-178994741
27	MAX	chr1:178994623-178995200	SK-N-SH	brain:	n/a	chr1:178995016-178995026
28	POLR2A	chr1:178994636-178995992	ECC-1	luminal epithelium:	n/a	n/a
29	ZNF143	chr1:178994183-178995707	H1-hESC	embryonic stem cell:	n/a	chr1:178994833-178994843
30	TAF1	chr1:178994555-178995853	H1-hESC	embryonic stem cell:	n/a	n/a
31	EP300	chr1:178994566-178995089	T-47D	breast:	n/a	chr1:178994709-178994723 chr1:178994838-178994847 chr1:178994834-178994843
32	CBX3	chr1:178993860-178995888	K562	blood:	n/a	n/a
33	PAX5	chr1:178994600-178995721	GM12878	blood:	n/a	chr1:178994836-178994845 chr1:178995683-178995692 chr1:178994772-178994781 chr1:178994779-178994788
34	MYC	chr1:178994603-178995878	H1-hESC	embryonic stem cell:	n/a	chr1:178995016-178995026
35	CREB1	chr1:178994612-178996093	HepG2	liver:	n/a	n/a
36	EP300	chr1:178994627-178995084	HepG2	liver:	n/a	chr1:178994709-178994723 chr1:178994838-178994847 chr1:178994834-178994843
37	CTCF	chr1:178994640-178994790	HCM	heart:	n/a	n/a
38	MAZ	chr1:178994626-178996058	GM12878	blood:	n/a	chr1:178995016-178995026
39	JUN	chr1:178994384-178995458	K562	blood:	n/a	chr1:178995018-178995027 chr1:178994770-178994779
40	HDAC2	chr1:178994614-178995889	K562	blood:	n/a	chr1:178994697-178994711 chr1:178994750-178994764 chr1:178994708-178994722 chr1:178995196-178995205 chr1:178994751-178994765
41	MYC	chr1:178994158-178996280	A549	lung:	n/a	chr1:178995016-178995026
42	SP1	chr1:178994604-178995547	H1-hESC	embryonic stem cell:	n/a	chr1:178995014-178995026 chr1:178995311-178995320 chr1:178995082-178995093 chr1:178995015-178995024 chr1:178995027-178995037 chr1:178994727-178994741
43	POLR2A	chr1:178994618-178996044	GM18951	blood:	n/a	n/a
44	IRF1	chr1:178994093-178997271	K562	blood:	n/a	chr1:178997164-178997181 chr1:178994771-178994780 chr1:178997184-178997191 chr1:178996939-178996952 chr1:178996142-178996156
45	EGR1	chr1:178994513-178996074	HCT-116	colon:	n/a	chr1:178995078-178995091 chr1:178995015-178995025 chr1:178995104-178995118 chr1:178994836-178994845 chr1:178995018-178995031
46	POLR2A	chr1:178994632-178996165	K562	blood:	n/a	n/a
47	EP300	chr1:178994597-178995314	ECC-1	luminal epithelium:	n/a	chr1:178994709-178994723 chr1:178994838-178994847 chr1:178994834-178994843
48	POLR2A	chr1:178994614-178996014	NB4	blood:	n/a	n/a
49	CHD2	chr1:178994420-178995923	K562	blood:	n/a	n/a
50	MYC	chr1:178994488-178996305	K562	blood:	n/a	chr1:178995016-178995026

No.	Distal block	Cell Line	Cell type
1	chr1:178994037..178996559-chr6:26216842..26218993,2	MCF-7	breast:
2	chr1:178510389..178513760-chr1:178993228..178995789,4	MCF-7	breast:
3	chr1:178993182..178999783-chr1:179045102..179052535,14	MCF-7	breast:
4	chr1:178693031..178696022-chr1:178993845..178996341,3	MCF-7	breast:

Variant related genes	Relation type
FAM20B	TF binding region
ENSG00000273062	Chromatin interaction
ENSG00000184909	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000213057	Chromatin interaction
ENSG00000116191	Chromatin interaction
ENSG00000186283	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10082052	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1046385	1.00[ASW][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap]
rs10913672	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11581232	0.80[AMR][1000 genomes]
rs1325194	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs2182102	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2296377	0.81[CHB][hapmap]
rs2636290	1.00[ASW][hapmap];0.81[MEX][hapmap]
rs28913887	1.00[YRI][hapmap]
rs28913889	1.00[YRI][hapmap]
rs3818433	1.00[ASW][hapmap]
rs4360489	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4652344	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4652348	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425512	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425515	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs6697029	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7532578	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7538498	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544801	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3420967	chr1:178993954-178996502	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	esv3396952	chr1:178994279-178996377	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3813638	GPR52	cis	parietal	SCAN
rs3813638	ABL2	cis	parietal	SCAN
rs3813638	TOR3A	cis	Artery Tibial	GTEx
rs3813638	RALGPS2	cis	parietal	SCAN
rs3813638	FAM20B	cis	parietal	SCAN
rs3813638	FAM20B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:178993400-178994800	Flanking Active TSS	K562	blood
2	chr1:178993600-178994800	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr1:178994000-178996200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:178994000-178996400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:178994200-178994800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:178994200-178994800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:178994200-178994800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr1:178994200-178994800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:178994200-178994800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:178994200-178994800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:178994200-178994800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:178994200-178994800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:178994200-178994800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr1:178994200-178994800	Flanking Active TSS	Fetal Muscle Trunk	muscle
15	chr1:178994200-178994800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:178994200-178994800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr1:178994200-178994800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr1:178994200-178994800	Flanking Active TSS	Dnd41	blood
19	chr1:178994200-178994800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr1:178994200-178995400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:178994200-178996000	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr1:178994200-178996000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:178994200-178996000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:178994200-178996000	Active TSS	Brain Hippocampus Middle	brain
25	chr1:178994200-178996000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:178994200-178996000	Active TSS	Rectal Smooth Muscle	rectum
27	chr1:178994200-178996200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:178994200-178996200	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr1:178994200-178996200	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr1:178994200-178996200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:178994200-178996200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:178994200-178996200	Active TSS	Fetal Lung	lung
33	chr1:178994200-178996200	Active TSS	Stomach Smooth Muscle	stomach
34	chr1:178994200-178996400	Active TSS	H9 Cell Line	embryonic stem cell
35	chr1:178994200-178996400	Active TSS	Aorta	Aorta
36	chr1:178994200-178996600	Active TSS	Colonic Mucosa	Colon
37	chr1:178994200-178996800	Active TSS	Psoas Muscle	Psoas
38	chr1:178994200-178996800	Active TSS	NHDF-Ad	bronchial
39	chr1:178994400-178994800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:178994400-178994800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr1:178994400-178994800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr1:178994400-178994800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr1:178994400-178994800	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr1:178994400-178994800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr1:178994400-178994800	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr1:178994400-178994800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:178994400-178994800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr1:178994400-178994800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr1:178994400-178994800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:178994400-178994800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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