Variant report

Variant	rs3738320
Chromosome Location	chr1:149982626-149982627
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	MYC	chr1:149982414-149983240	K562	blood:	n/a	n/a
2	YY1	chr1:149982099-149982953	HepG2	liver:	n/a	chr1:149982649-149982663
3	SRF	chr1:149982548-149982850	GM12878	blood:	n/a	n/a
4	REST	chr1:149982472-149982958	SK-N-SH	brain:	n/a	chr1:149982798-149982811
5	GABPA	chr1:149982389-149982981	H1-hESC	embryonic stem cell:	n/a	n/a
6	FOS	chr1:149982566-149982820	MCF10A-Er-Src	breast:	n/a	n/a
7	EGR1	chr1:149982475-149982961	ECC-1	luminal epithelium:	n/a	chr1:149982744-149982757
8	SIN3AK20	chr1:149980554-149983301	MCF-7	breast:	n/a	n/a
9	GABPA	chr1:149981674-149983374	MCF-7	breast:	n/a	n/a
10	TEAD4	chr1:149982278-149983115	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr1:149981771-149982970	H1-neurons	neurons:	n/a	n/a
12	MAZ	chr1:149982224-149983053	GM12878	blood:	n/a	n/a
13	EGR1	chr1:149982390-149982988	K562	blood:	n/a	chr1:149982744-149982757
14	POLR2A	chr1:149982465-149983007	MCF10A-Er-Src	breast:	n/a	n/a
15	REST	chr1:149982399-149982854	SK-N-SH	brain:	n/a	chr1:149982798-149982811
16	POLR2A	chr1:149982345-149983000	GM12878	blood:	n/a	n/a
17	FOSL2	chr1:149982418-149983062	A549	lung:	n/a	n/a
18	SMARCC1	chr1:149981227-149983065	Hela-S3	cervix:	n/a	n/a
19	MYBL2	chr1:149982386-149983136	HepG2	liver:	n/a	n/a
20	GATA1	chr1:149981206-149983090	PBDE	blood:	n/a	chr1:149981447-149981457 chr1:149981447-149981456 chr1:149981444-149981460 chr1:149981449-149981456 chr1:149981449-149981459 chr1:149981442-149981463
21	CTCF	chr1:149982580-149982730	WERI-Rb-1	eye:	n/a	n/a
22	EGR1	chr1:149982446-149982947	H1-hESC	embryonic stem cell:	n/a	chr1:149982744-149982757
23	CTCF	chr1:149982500-149982650	HCFaa	heart:	n/a	n/a
24	PML	chr1:149982523-149982964	GM12878	blood:	n/a	n/a
25	HA-E2F1	chr1:149982488-149982992	Hela-S3	cervix:	n/a	chr1:149982653-149982663 chr1:149982818-149982825 chr1:149982758-149982769 chr1:149982763-149982772
26	TAF1	chr1:149982310-149983018	K562	blood:	n/a	n/a
27	SP1	chr1:149982425-149982857	H1-hESC	embryonic stem cell:	n/a	chr1:149982494-149982503 chr1:149982764-149982776 chr1:149982764-149982776 chr1:149982765-149982774 chr1:149982493-149982503 chr1:149982493-149982502 chr1:149982492-149982504 chr1:149982492-149982504
28	SIN3AK20	chr1:149981962-149982975	PANC-1	pancreas:	n/a	n/a
29	MBD4	chr1:149982431-149982973	HepG2	liver:	n/a	n/a
30	RCOR1	chr1:149981630-149982988	K562	blood:	n/a	n/a
31	NFIC	chr1:149982470-149982953	GM12878	blood:	n/a	n/a
32	MYC	chr1:149982615-149982829	K562	blood:	n/a	n/a
33	CTBP2	chr1:149982050-149982907	H1-hESC	embryonic stem cell:	n/a	n/a
34	USF1	chr1:149982435-149983077	A549	lung:	n/a	n/a
35	CHD2	chr1:149982367-149982941	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:149982411-149983062	K562	blood:	n/a	n/a
37	POLR2A	chr1:149982398-149982961	H1-hESC	embryonic stem cell:	n/a	n/a
38	SMC3	chr1:149981541-149983075	Hela-S3	cervix:	n/a	n/a
39	YY1	chr1:149981697-149982850	ECC-1	luminal epithelium:	n/a	chr1:149982649-149982663
40	POLR2A	chr1:149982193-149982983	HUVEC	blood vessel:	n/a	n/a
41	TRIM28	chr1:149982375-149983059	K562	blood:	n/a	n/a
42	GTF2F1	chr1:149982509-149982865	K562	blood:	n/a	n/a
43	EP300	chr1:149982590-149983063	K562	blood:	n/a	n/a
44	RELA	chr1:149982538-149983136	GM19099	blood:	n/a	n/a
45	GATA3	chr1:149981490-149983140	MCF-7	breast:	n/a	n/a
46	POLR2A	chr1:149981428-149983081	Hela-S3	cervix:	n/a	n/a
47	TAF1	chr1:149982473-149982820	GM12891	blood:	n/a	n/a
48	FOS	chr1:149982533-149982998	HUVEC	blood vessel:	n/a	n/a
49	RCOR1	chr1:149982396-149982866	HepG2	liver:	n/a	n/a
50	MTA3	chr1:149981495-149983136	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:149853005..149861438-chr1:149978765..149991065,34	MCF-7	breast:
2	chr1:149870476..149872872-chr1:149980684..149982893,3	MCF-7	breast:
3	chr1:149980635..149983433-chr1:150127638..150130379,2	K562	blood:
4	chr1:149898259..149901942-chr1:149980885..149984493,5	MCF-7	breast:
5	chr1:149980215..149984264-chr1:150036474..150041542,10	K562	blood:
6	chr1:149855536..149863300-chr1:149977462..149985642,29	K562	blood:
7	chr1:149977821..149984701-chr1:150037094..150041280,13	MCF-7	breast:
8	chr1:149981175..149982932-chr1:150039721..150041542,2	K562	blood:
9	chr1:149982249..149983161-chr11:93474176..93474723,2	Hela-S3	cervix:
10	chr1:149854540..149863300-chr1:149979575..149985253,19	K562	blood:
11	chr1:149815281..149817675-chr1:149980545..149983333,2	K562	blood:
12	chr1:149857288..149861878-chr1:149980292..149985449,12	MCF-7	breast:
13	chr1:149982480..149983168-chr11:31531157..31531798,2	Hela-S3	cervix:
14	chr1:149982316..149983111-chr1:150039258..150039856,2	MCF-7	breast:
15	chr1:149982029..149982749-chr16:70285430..70285983,2	Hela-S3	cervix:
16	chr1:149896924..149901430-chr1:149978916..149983998,7	MCF-7	breast:
17	chr1:149981726..149982724-chr7:6120850..6121372,2	Hela-S3	cervix:
18	chr1:149908458..149914088-chr1:149980717..149984285,8	MCF-7	breast:
19	chr1:149982208..149982928-chr1:150038867..150039793,2	MCF-7	breast:
20	chr1:149982260..149984112-chr1:150253669..150255654,2	MCF-7	breast:
21	chr1:149980534..149984301-chr1:150205783..150209955,5	K562	blood:

Variant related genes	Relation type
OTUD7B	TF binding region
ENSG00000184260	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000014914	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000231704	Chromatin interaction
ENSG00000272993	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000166012	Chromatin interaction
ENSG00000136631	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000148950	Chromatin interaction
ENSG00000223496	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000159208	Chromatin interaction
ENSG00000109911	Chromatin interaction
ENSG00000143368	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10494260	0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11205309	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11205310	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12022928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12023231	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs12023748	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12026500	0.90[ASN][1000 genomes]
rs12082689	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409885	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs16835135	0.85[YRI][hapmap]
rs1868992	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs3767627	0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3767628	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3936952	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926386	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs4926400	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs58700306	0.83[AMR][1000 genomes]
rs6660842	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72692821	0.85[ASN][1000 genomes]
rs7544531	0.89[ASW][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs7551741	0.86[ASN][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	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3738320	SCNM1	cis	parietal	SCAN
rs3738320	MRPS21	cis	parietal	SCAN
rs3738320	VPS72	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149977800-149983200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:149980000-149983200	Active TSS	Right Atrium	heart
3	chr1:149980200-149983000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:149980200-149983000	Active TSS	Brain Anterior Caudate	brain
5	chr1:149980200-149983000	Active TSS	Brain Hippocampus Middle	brain
6	chr1:149980200-149983200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr1:149980400-149983000	Active TSS	Aorta	Aorta
8	chr1:149980600-149983000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:149980600-149983000	Active TSS	Brain Cingulate Gyrus	brain
10	chr1:149980600-149983000	Active TSS	Brain Substantia Nigra	brain
11	chr1:149980600-149983000	Active TSS	Stomach Mucosa	stomach
12	chr1:149980600-149983000	Active TSS	NHLF	lung
13	chr1:149980600-149983200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr1:149980600-149983200	Active TSS	Psoas Muscle	Psoas
15	chr1:149980800-149982800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:149980800-149982800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:149980800-149983000	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:149980800-149983000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:149980800-149983000	Active TSS	Duodenum Mucosa	Duodenum
20	chr1:149980800-149983000	Active TSS	Fetal Intestine Large	intestine
21	chr1:149980800-149983000	Active TSS	Left Ventricle	heart
22	chr1:149980800-149983000	Active TSS	Lung	lung
23	chr1:149980800-149983200	Active TSS	H9 Cell Line	embryonic stem cell
24	chr1:149980800-149983200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:149980800-149983200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:149980800-149983200	Active TSS	Colonic Mucosa	Colon
27	chr1:149980800-149983200	Active TSS	Right Ventricle	heart
28	chr1:149980800-149983600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:149981000-149982800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:149981000-149982800	Active TSS	NH-A	brain
31	chr1:149981000-149983000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:149981000-149983000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:149981000-149983000	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr1:149981000-149983000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:149981000-149983000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:149981000-149983000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:149981000-149983000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:149981000-149983000	Active TSS	Fetal Intestine Small	intestine
39	chr1:149981000-149983000	Active TSS	Fetal Kidney	kidney
40	chr1:149981000-149983000	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr1:149981000-149983000	Active TSS	GM12878-XiMat	blood
42	chr1:149981000-149983000	Active TSS	HSMM	muscle
43	chr1:149981000-149983000	Active TSS	HSMMtube	muscle
44	chr1:149981000-149983000	Active TSS	K562	blood
45	chr1:149981000-149983000	Active TSS	NHDF-Ad	bronchial
46	chr1:149981000-149983200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:149981000-149983200	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr1:149981000-149983200	Active TSS	Fetal Muscle Trunk	muscle
49	chr1:149981000-149983200	Active TSS	Ovary	ovary
50	chr1:149981000-149983400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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