Variant report

Variant	rs316643
Chromosome Location	chr1:84764475-84764476
allele	C/G
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	chr1:84764050-84764881	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:84764040-84765057	GM15510	blood:	n/a	n/a
3	CTBP2	chr1:84763884-84765083	H1-hESC	embryonic stem cell:	n/a	n/a
4	UBTF	chr1:84764156-84764924	K562	blood:	n/a	n/a
5	TCF12	chr1:84763959-84764888	ECC-1	luminal epithelium:	n/a	chr1:84764485-84764495
6	SMARCB1	chr1:84764041-84765263	Hela-S3	cervix:	n/a	chr1:84764140-84764149
7	POLR2A	chr1:84764012-84765123	Gliobla	brain:	n/a	n/a
8	POLR2A	chr1:84764052-84765330	K562	blood:	n/a	n/a
9	MAZ	chr1:84763581-84765322	IMR90	lung:	n/a	n/a
10	POLR2A	chr1:84764110-84764562	A549	lung:	n/a	n/a
11	TCF7L2	chr1:84764034-84765087	Hela-S3	cervix:	n/a	chr1:84764307-84764321 chr1:84764308-84764322
12	HDAC2	chr1:84764081-84764520	K562	blood:	n/a	n/a
13	TEAD4	chr1:84763974-84764484	K562	blood:	n/a	n/a
14	MXI1	chr1:84763790-84765164	IMR90	lung:	n/a	n/a
15	YY1	chr1:84764438-84764942	GM12891	blood:	n/a	chr1:84764452-84764463 chr1:84764862-84764876
16	MAX	chr1:84763960-84765183	A549	lung:	n/a	n/a
17	TAF1	chr1:84764444-84765118	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:84764104-84764947	GM12878	blood:	n/a	n/a
19	MAX	chr1:84763987-84764630	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:84764019-84765615	K562	blood:	n/a	n/a
21	RCOR1	chr1:84764310-84764658	K562	blood:	n/a	n/a
22	PML	chr1:84763965-84764901	K562	blood:	n/a	n/a
23	HMGN3	chr1:84764001-84765191	K562	blood:	n/a	n/a
24	TAF1	chr1:84764110-84765065	SK-N-SH	brain:	n/a	n/a
25	MAX	chr1:84763965-84764656	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:84764062-84764890	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr1:84763935-84765458	HL-60	blood:	n/a	n/a
28	MAX	chr1:84763944-84765180	SK-N-SH	brain:	n/a	n/a
29	MAX	chr1:84763879-84765253	A549	lung:	n/a	n/a
30	POLR2A	chr1:84764076-84765353	K562	blood:	n/a	n/a
31	ZNF143	chr1:84763892-84765238	K562	blood:	n/a	chr1:84764142-84764151 chr1:84764140-84764158 chr1:84764699-84764709 chr1:84764140-84764149
32	POLR2A	chr1:84764019-84765784	Raji	blood:	n/a	n/a
33	POLR2A	chr1:84764062-84764876	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr1:84763955-84765055	K562	blood:	n/a	n/a
35	POLR2A	chr1:84764161-84764475	H1-hESC	embryonic stem cell:	n/a	n/a
36	YY1	chr1:84764067-84764999	K562	blood:	n/a	chr1:84764452-84764463 chr1:84764198-84764209 chr1:84764226-84764240 chr1:84764862-84764876
37	ETS1	chr1:84763990-84764579	K562	blood:	n/a	chr1:84764138-84764151 chr1:84764143-84764150 chr1:84764139-84764152
38	BHLHE40	chr1:84764011-84765256	K562	blood:	n/a	chr1:84764122-84764138 chr1:84764862-84764878
39	PAX5	chr1:84764353-84764902	GM12892	blood:	n/a	n/a
40	POLR2A	chr1:84764020-84764995	HUVEC	blood vessel:	n/a	n/a
41	MAX	chr1:84763996-84764501	MCF-7	breast:	n/a	n/a
42	MTA3	chr1:84764047-84765327	GM12878	blood:	n/a	n/a
43	ZNF263	chr1:84764022-84765211	HEK293-T-REx	kidney:	n/a	n/a
44	HEY1	chr1:84764030-84765325	K562	blood:	n/a	chr1:84764195-84764210 chr1:84764172-84764187
45	REST	chr1:84763964-84765073	HL-60	blood:	n/a	chr1:84764382-84764400 chr1:84764668-84764688 chr1:84764459-84764472 chr1:84764455-84764475 chr1:84764462-84764475 chr1:84764459-84764472 chr1:84764110-84764123
46	UBTF	chr1:84764062-84765146	K562	blood:	n/a	n/a
47	POLR2A	chr1:84764078-84765295	K562	blood:	n/a	n/a
48	TAF1	chr1:84763934-84765073	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr1:84764010-84764502	K562	blood:	n/a	n/a
50	YY1	chr1:84764045-84764938	NT2-D1	testis:	n/a	chr1:84764452-84764463 chr1:84764198-84764209 chr1:84764226-84764240 chr1:84764862-84764876

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84763327..84765739-chr1:84765755..84771723,8	K562	blood:
2	chr1:84764306..84766033-chr1:84791086..84793194,2	MCF-7	breast:

Variant related genes	Relation type
SAMD13	TF binding region
ENSG00000203943	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1085093	0.81[EUR][1000 genomes]
rs12037040	0.92[ASN][1000 genomes]
rs12041053	0.93[ASN][1000 genomes]
rs12564352	0.92[ASN][1000 genomes]
rs184358	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316637	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316639	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs316644	0.93[ASN][1000 genomes]
rs58205457	0.92[ASN][1000 genomes]
rs6698676	0.92[ASN][1000 genomes]
rs784830	0.81[EUR][1000 genomes]
rs784831	0.81[EUR][1000 genomes]
rs784832	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs784833	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84762000-84766000	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr1:84762400-84765800	Active TSS	Rectal Smooth Muscle	rectum
3	chr1:84762600-84765600	Active TSS	Duodenum Mucosa	Duodenum
4	chr1:84762600-84765800	Active TSS	Colonic Mucosa	Colon
5	chr1:84762800-84764800	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr1:84763000-84765800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr1:84763200-84765200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr1:84763200-84765200	Active TSS	Gastric	stomach
9	chr1:84763200-84769400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:84763400-84765000	Active TSS	Pancreas	Pancrea
11	chr1:84763400-84765400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:84763400-84765800	Active TSS	Small Intestine	intestine
13	chr1:84763600-84764800	Active TSS	Brain Germinal Matrix	brain
14	chr1:84763600-84764800	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr1:84763600-84764800	Active TSS	NH-A	brain
16	chr1:84763600-84765000	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr1:84763600-84765000	Active TSS	Stomach Smooth Muscle	stomach
18	chr1:84763600-84765000	Active TSS	NHDF-Ad	bronchial
19	chr1:84763600-84765200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:84763600-84765200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr1:84763600-84765400	Active TSS	GM12878-XiMat	blood
22	chr1:84763600-84765600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr1:84763600-84765600	Active TSS	A549	lung
24	chr1:84763800-84764600	Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr1:84763800-84764600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:84763800-84764800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:84763800-84764800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr1:84763800-84764800	Active TSS	Fetal Muscle Leg	muscle
29	chr1:84763800-84764800	Active TSS	HMEC	breast
30	chr1:84763800-84764800	Active TSS	NHEK	skin
31	chr1:84763800-84765000	Active TSS	H1 Cell Line	embryonic stem cell
32	chr1:84763800-84765000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:84763800-84765000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:84763800-84765000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:84763800-84765000	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr1:84763800-84765000	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr1:84763800-84765000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:84763800-84765000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:84763800-84765000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:84763800-84765000	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr1:84763800-84765000	Active TSS	Muscle Satellite Cultured Cells	--
42	chr1:84763800-84765000	Active TSS	Brain Angular Gyrus	brain
43	chr1:84763800-84765000	Active TSS	Brain Hippocampus Middle	brain
44	chr1:84763800-84765000	Active TSS	Fetal Brain Female	brain
45	chr1:84763800-84765000	Active TSS	Fetal Heart	heart
46	chr1:84763800-84765000	Active TSS	Fetal Intestine Large	intestine
47	chr1:84763800-84765000	Active TSS	Fetal Kidney	kidney
48	chr1:84763800-84765000	Active TSS	Fetal Thymus	thymus
49	chr1:84763800-84765000	Active TSS	Right Ventricle	heart
50	chr1:84763800-84765000	Active TSS	K562	blood

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