Variant report

Variant	rs546445
Chromosome Location	chr1:93544629-93544630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:640)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:640 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr1:93544431-93545032	A549	lung:	n/a	n/a
2	GABPA	chr1:93544456-93545232	A549	lung:	n/a	n/a
3	TRIM28	chr1:93544310-93545123	K562	blood:	n/a	n/a
4	CTCF	chr1:93544600-93544750	HA-sp	spinal cord:	n/a	n/a
5	ETS1	chr1:93544433-93545215	A549	lung:	n/a	n/a
6	POLR2A	chr1:93543983-93545604	HUVEC	blood vessel:	n/a	n/a
7	NFIC	chr1:93544160-93545317	GM12878	blood:	n/a	n/a
8	MAX	chr1:93544307-93545181	HepG2	liver:	n/a	n/a
9	REST	chr1:93544339-93545107	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:93544400-93545231	U87	brain:	n/a	n/a
11	POLR2A	chr1:93544098-93545753	H1-neurons	neurons:	n/a	n/a
12	CTCF	chr1:93544600-93544750	WERI-Rb-1	eye:	n/a	n/a
13	YY1	chr1:93544426-93545267	GM12891	blood:	n/a	n/a
14	CHD2	chr1:93544447-93545110	K562	blood:	n/a	n/a
15	UBTF	chr1:93544456-93546261	K562	blood:	n/a	n/a
16	NR2F2	chr1:93544508-93545023	K562	blood:	n/a	n/a
17	SIN3AK20	chr1:93544369-93545002	PFSK-1	brain:	n/a	n/a
18	EP300	chr1:93544504-93545029	GM12878	blood:	n/a	n/a
19	SIN3AK20	chr1:93544244-93545308	MCF-7	breast:	n/a	n/a
20	POLR2A	chr1:93544102-93545528	HUVEC	blood vessel:	n/a	n/a
21	MXI1	chr1:93543964-93545111	GM12878	blood:	n/a	n/a
22	JUND	chr1:93544451-93545127	A549	lung:	n/a	chr1:93544768-93544777
23	ZC3H11A	chr1:93544612-93545284	K562	blood:	n/a	n/a
24	MAX	chr1:93544441-93544936	H1-hESC	embryonic stem cell:	n/a	n/a
25	RELA	chr1:93544116-93545291	GM19099	blood:	n/a	n/a
26	TBP	chr1:93544236-93545714	H1-hESC	embryonic stem cell:	n/a	n/a
27	JUND	chr1:93544429-93545093	MCF-7	breast:	n/a	chr1:93544768-93544777
28	MEF2A	chr1:93544416-93545033	GM12878	blood:	n/a	n/a
29	ELK1	chr1:93544311-93545079	GM12878	blood:	n/a	n/a
30	PAX5	chr1:93544492-93544979	GM12891	blood:	n/a	n/a
31	REST	chr1:93544461-93545005	SK-N-SH	brain:	n/a	n/a
32	CEBPD	chr1:93544481-93544861	HepG2	liver:	n/a	n/a
33	PAX5	chr1:93544473-93544917	GM12878	blood:	n/a	n/a
34	TCF7L2	chr1:93544305-93545094	PANC-1	pancreas:	n/a	n/a
35	REST	chr1:93544451-93545007	PANC-1	pancreas:	n/a	n/a
36	RAD21	chr1:93544613-93544800	K562	blood:	n/a	n/a
37	POLR2A	chr1:93544423-93545003	HepG2	liver:	n/a	n/a
38	MYC	chr1:93544528-93544944	K562	blood:	n/a	n/a
39	EGR1	chr1:93544561-93544841	GM12878	blood:	n/a	chr1:93544562-93544575
40	POLR2A	chr1:93544141-93545654	K562	blood:	n/a	n/a
41	YY1	chr1:93544507-93545028	A549	lung:	n/a	n/a
42	EP300	chr1:93544410-93545048	K562	blood:	n/a	n/a
43	POLR2A	chr1:93544302-93545171	MCF-7	breast:	n/a	n/a
44	EP300	chr1:93544290-93545041	A549	lung:	n/a	n/a
45	CREB1	chr1:93544327-93545669	H1-hESC	embryonic stem cell:	n/a	n/a
46	REST	chr1:93544509-93544808	Hela-S3	cervix:	n/a	n/a
47	KAP1	chr1:93544213-93545239	HEK293	kidney:	n/a	n/a
48	POLR2A	chr1:93543787-93545840	GM12878	blood:	n/a	n/a
49	CEBPD	chr1:93544359-93545132	K562	blood:	n/a	n/a
50	FOS	chr1:93544585-93544895	MCF10A-Er-Src	breast:	n/a	chr1:93544768-93544777

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:93487223..93489014-chr1:93543210..93544783,2	K562	blood:
2	chr1:45186972..45187847-chr1:93544155..93544946,2	NB4	blood:
3	chr1:93296271..93298475-chr1:93543770..93546056,2	MCF-7	breast:
4	chr1:93542830..93545559-chr20:45984443..45987122,2	MCF-7	breast:
5	chr1:93544000..93546020-chr1:94311349..94313397,2	MCF-7	breast:
6	chr1:93543004..93547095-chr1:93643826..93649088,10	K562	blood:
7	chr1:93544165..93544880-chr11:82867978..82868654,2	HCT-116	colon:
8	chr1:93543004..93547588-chr1:93644888..93649088,6	K562	blood:
9	chr1:93296486..93299108-chr1:93543311..93545320,3	K562	blood:
10	chr1:93296076..93299049-chr1:93541677..93546567,5	K562	blood:
11	chr1:93544179..93544991-chr2:9695701..9696695,2	NB4	blood:
12	chr1:93544361..93545010-chr21:37692130..37693015,2	HCT-116	colon:
13	chr1:93543927..93545832-chr1:93912304..93915209,2	K562	blood:

No data

Variant related genes	Relation type
MTF2	TF binding region
ENSG00000101040	Chromatin interaction
ENSG00000151694	Chromatin interaction
ENSG00000271855	Chromatin interaction
ENSG00000165494	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000117500	Chromatin interaction
ENSG00000273199	Chromatin interaction
ENSG00000159256	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000122483	Chromatin interaction
ENSG00000137942	Chromatin interaction
ENSG00000122406	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11164869	0.93[CEU][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12062154	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12080248	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12736775	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2391228	0.96[EUR][1000 genomes]
rs2749734	0.92[ASN][1000 genomes]
rs2785602	0.97[ASN][1000 genomes]
rs2785605	0.97[ASN][1000 genomes]
rs2815419	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2815423	0.97[ASN][1000 genomes]
rs2815424	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs488345	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs490153	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs495580	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs500349	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs502651	0.87[ASN][1000 genomes]
rs519319	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs539544	0.97[ASN][1000 genomes]
rs548751	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs550892	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs566843	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs580828	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6670960	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696026	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6702666	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6703169	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7555395	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs797594	0.86[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs546445	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs546445	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs546445	TMED5	cis	cerebellum	SCAN
rs546445	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs546445	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs546445	CCDC18	Cis_1M	lymphoblastoid	RTeQTL
rs546445	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs546445	RP4-717I23.3	cis	Artery Tibial	GTEx
rs546445	RP4-717I23.3	cis	Artery Aorta	GTEx
rs546445	RP4-717I23.3	cis	lung	GTEx
rs546445	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs546445	RP4-717I23.3	cis	Whole Blood	GTEx
rs546445	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs546445	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs546445	TMED5	cis	parietal	SCAN
rs546445	RP4-717I23.3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93543800-93545000	Active TSS	Fetal Brain Female	brain
2	chr1:93543800-93545600	Active TSS	Colon Smooth Muscle	Colon
3	chr1:93543800-93546000	Active TSS	Placenta Amnion	Placenta Amnion
4	chr1:93543800-93546200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:93543800-93546400	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr1:93543800-93546600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:93543800-93546800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:93543800-93546800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:93543800-93546800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:93543800-93547400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:93543800-93547400	Active TSS	Fetal Kidney	kidney
12	chr1:93544000-93545000	Active TSS	Brain Germinal Matrix	brain
13	chr1:93544000-93545400	Active TSS	Osteobl	bone
14	chr1:93544000-93545800	Active TSS	Rectal Smooth Muscle	rectum
15	chr1:93544000-93546000	Active TSS	Placenta	Placenta
16	chr1:93544000-93546400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:93544000-93546400	Active TSS	Fetal Muscle Trunk	muscle
18	chr1:93544000-93546400	Active TSS	Ovary	ovary
19	chr1:93544000-93546600	Active TSS	H9 Cell Line	embryonic stem cell
20	chr1:93544000-93546600	Active TSS	NHDF-Ad	bronchial
21	chr1:93544000-93546800	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr1:93544000-93547000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:93544000-93547000	Active TSS	Fetal Stomach	stomach
24	chr1:93544000-93547000	Active TSS	K562	blood
25	chr1:93544000-93547200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:93544000-93547200	Active TSS	A549	lung
27	chr1:93544000-93547200	Active TSS	HSMM	muscle
28	chr1:93544000-93547400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:93544000-93547400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:93544000-93547400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:93544000-93547600	Active TSS	H1 Cell Line	embryonic stem cell
32	chr1:93544000-93547600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:93544000-93548000	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr1:93544200-93545000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:93544200-93545400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:93544200-93545400	Active TSS	Liver	Liver
37	chr1:93544200-93545800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:93544200-93545800	Active TSS	Left Ventricle	heart
39	chr1:93544200-93545800	Active TSS	Pancreas	Pancrea
40	chr1:93544200-93546000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:93544200-93546000	Active TSS	Small Intestine	intestine
42	chr1:93544200-93546200	Active TSS	Aorta	Aorta
43	chr1:93544200-93546200	Active TSS	Brain Angular Gyrus	brain
44	chr1:93544200-93546400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:93544200-93546400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:93544200-93546400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:93544200-93546400	Active TSS	Colonic Mucosa	Colon
48	chr1:93544200-93546400	Active TSS	Fetal Heart	heart
49	chr1:93544200-93546400	Active TSS	Psoas Muscle	Psoas
50	chr1:93544200-93546400	Active TSS	Right Ventricle	heart

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