Variant report

Variant	rs17046778
Chromosome Location	chr2:55459373-55459374
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	POLR2A	chr2:55458996-55460836	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr2:55458744-55464800	K562	blood:	n/a	n/a
3	ELF1	chr2:55458669-55460096	A549	lung:	n/a	chr2:55459306-55459319
4	CEBPB	chr2:55459053-55460191	GM12878	blood:	n/a	n/a
5	REST	chr2:55458997-55459547	K562	blood:	n/a	n/a
6	POLR2A	chr2:55458967-55461056	K562	blood:	n/a	n/a
7	SP1	chr2:55459014-55459970	H1-hESC	embryonic stem cell:	n/a	n/a
8	RUNX3	chr2:55458943-55460719	GM12878	blood:	n/a	n/a
9	TCF12	chr2:55458907-55460413	ECC-1	luminal epithelium:	n/a	n/a
10	GATA3	chr2:55459242-55459463	SH-SY5Y	brain:	n/a	n/a
11	MAFK	chr2:55459272-55460015	HepG2	liver:	n/a	n/a
12	RELA	chr2:55459328-55460378	GM12892	blood:	n/a	n/a
13	MYC	chr2:55459255-55460629	K562	blood:	n/a	n/a
14	YY1	chr2:55459022-55459577	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr2:55458959-55464692	GM12878	blood:	n/a	n/a
16	CHD2	chr2:55458909-55460030	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr2:55458937-55460460	A549	lung:	n/a	chr2:55459829-55459849
18	POLR2A	chr2:55458934-55460788	U87	brain:	n/a	n/a
19	HEY1	chr2:55459065-55461114	K562	blood:	n/a	n/a
20	SMARCC1	chr2:55458745-55460606	Hela-S3	cervix:	n/a	chr2:55459487-55459496
21	SPI1	chr2:55459202-55459927	HL-60	blood:	n/a	n/a
22	ZKSCAN1	chr2:55459125-55460469	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr2:55458747-55464848	U87	brain:	n/a	n/a
24	MTA3	chr2:55458589-55461547	GM12878	blood:	n/a	n/a
25	MYC	chr2:55459245-55460439	K562	blood:	n/a	n/a
26	HCFC1	chr2:55458624-55460325	K562	blood:	n/a	n/a
27	GABPA	chr2:55459122-55459537	K562	blood:	n/a	chr2:55459343-55459350
28	POLR2A	chr2:55458977-55460394	H1-neurons	neurons:	n/a	n/a
29	ELF1	chr2:55458502-55460607	HCT-116	colon:	n/a	chr2:55459306-55459319
30	TBP	chr2:55459098-55460493	GM12878	blood:	n/a	n/a
31	SRF	chr2:55458647-55459625	ECC-1	luminal epithelium:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
32	MAX	chr2:55459161-55460475	H1-hESC	embryonic stem cell:	n/a	n/a
33	GTF2F1	chr2:55459122-55460114	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr2:55458731-55465585	GM12891	blood:	n/a	n/a
35	POLR2A	chr2:55459010-55461927	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr2:55459152-55460219	K562	blood:	n/a	n/a
37	SP4	chr2:55459055-55460290	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr2:55458583-55460929	A549	lung:	n/a	n/a
39	EP300	chr2:55458841-55460139	A549	lung:	n/a	chr2:55459308-55459315
40	POLR2A	chr2:55458589-55462559	HCT-116	colon:	n/a	n/a
41	SIN3AK20	chr2:55458980-55460006	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr2:55458976-55460642	ProgFib	skin:	n/a	n/a
43	GATA3	chr2:55459169-55459556	T-47D	breast:	n/a	n/a
44	MAX	chr2:55458827-55460650	Hela-S3	cervix:	n/a	n/a
45	MAFK	chr2:55458993-55459997	Hela-S3	cervix:	n/a	chr2:55459207-55459221
46	ELF1	chr2:55459193-55460069	SK-N-SH	brain:	n/a	chr2:55459306-55459319
47	POLR2A	chr2:55459082-55460051	HepG2	liver:	n/a	n/a
48	POLR2A	chr2:55458627-55465420	H1-hESC	embryonic stem cell:	n/a	n/a
49	RAD21	chr2:55459133-55460068	IMR90	lung:	n/a	n/a
50	SIX5	chr2:55459256-55459905	K562	blood:	n/a	chr2:55459485-55459499 chr2:55459489-55459498 chr2:55459487-55459496

No.	Distal block	Cell Line	Cell type
1	chr2:55458112..55461105-chr2:55507986..55510921,3	MCF-7	breast:
2	chr2:55459243..55461012-chr2:55645151..55647509,2	MCF-7	breast:
3	chr12:110338094..110338823-chr2:55458974..55459662,2	Hela-S3	cervix:
4	chr2:54195792..54198215-chr2:55457941..55460893,2	K562	blood:
5	chr2:55275304..55279887-chr2:55458370..55461390,5	K562	blood:
6	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
7	chr2:55276121..55279274-chr2:55457448..55460901,6	K562	blood:
8	chr2:55458256..55461079-chr2:55494634..55496499,3	K562	blood:
9	chr2:55458277..55462347-chr2:55843080..55846218,4	K562	blood:
10	chr11:76155250..76155837-chr2:55459276..55459949,2	Hela-S3	cervix:
11	chr2:55458156..55461118-chr2:55494163..55499368,6	MCF-7	breast:
12	chr12:10765822..10766366-chr2:55459151..55460039,2	HCT-116	colon:
13	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:
14	chr16:67207875..67208482-chr2:55459236..55460116,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTIF2-3	chr2:55459372-55459439	NONHSAT070763
2	lnc-MTIF2-3	chr2:55459372-55459428	NONHSAT070768
3	lnc-MTIF2-3	chr2:55459372-55459399	NONHSAT070767

Variant related genes	Relation type
RPS27A	TF binding region
CLHC1	TF binding region
ENSG00000139437	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000255135	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000140939	Chromatin interaction
ENSG00000115355	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000111196	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000162997	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs17852670	0.83[AMR][1000 genomes]
rs2576722	0.83[ASN][1000 genomes]
rs2920965	0.88[ASN][1000 genomes]
rs4435493	0.83[AMR][1000 genomes]
rs57529275	0.86[ASN][1000 genomes]
rs57681837	0.95[ASN][1000 genomes]
rs59439819	0.93[ASN][1000 genomes]
rs61109509	0.95[ASN][1000 genomes]
rs61486882	0.84[ASN][1000 genomes]
rs6706815	0.81[AMR][1000 genomes]
rs6726380	0.93[ASN][1000 genomes]
rs7349360	0.91[ASN][1000 genomes]
rs7349405	0.84[ASN][1000 genomes]
rs934709	0.83[AMR][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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs17046778	CLHC1	cis	Esophagus Mucosa	GTEx
rs17046778	CLHC1	cis	Artery Tibial	GTEx
rs17046778	CLHC1	cis	Adipose Subcutaneous	GTEx
rs17046778	CLHC1	cis	Esophagus Muscularis	GTEx
rs17046778	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs17046778	CLHC1	cis	Artery Aorta	GTEx
rs17046778	CLHC1	cis	Stomach	GTEx
rs17046778	CLHC1	cis	Nerve Tibial	GTEx
rs17046778	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs17046778	CLHC1	cis	Muscle Skeletal	GTEx
rs17046778	CLHC1	cis	Whole Blood	GTEx
rs17046778	CLHC1	cis	Heart Left Ventricle	GTEx
rs17046778	ENSG00000162994	cis	multi-tissue	Pritchard
rs17046778	CLHC1	cis	lung	GTEx
rs17046778	CLHC1	cis	Thyroid	GTEx
rs17046778	C2orf63	cis	multi-tissue	Pritchard
rs17046778	AC012358.7	cis	Adipose Subcutaneous	GTEx
rs17046778	C2orf63	cis	intralobular white matter	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55457800-55460000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr2:55457800-55460400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:55457800-55460400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr2:55458000-55460200	Active TSS	A549	lung
5	chr2:55458000-55460400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:55458200-55460000	Active TSS	K562	blood
7	chr2:55458200-55460200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:55458200-55460400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:55458200-55460600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:55458200-55460800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:55458200-55460800	Active TSS	HMEC	breast
12	chr2:55458400-55459400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:55458400-55459400	Flanking Active TSS	Liver	Liver
14	chr2:55458400-55459800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr2:55458400-55460200	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr2:55458400-55460200	Active TSS	Stomach Smooth Muscle	stomach
17	chr2:55458400-55460400	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr2:55458400-55460400	Active TSS	H1 Cell Line	embryonic stem cell
19	chr2:55458400-55460400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:55458400-55460400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:55458400-55460600	Active TSS	H9 Cell Line	embryonic stem cell
22	chr2:55458400-55460600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:55458400-55460600	Active TSS	Aorta	Aorta
24	chr2:55458400-55460600	Active TSS	Fetal Stomach	stomach
25	chr2:55458400-55460600	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr2:55458400-55460600	Active TSS	Right Atrium	heart
27	chr2:55458400-55460600	Active TSS	GM12878-XiMat	blood
28	chr2:55458400-55460600	Active TSS	HSMM	muscle
29	chr2:55458400-55460600	Active TSS	NH-A	brain
30	chr2:55458400-55460600	Active TSS	NHLF	lung
31	chr2:55458400-55460800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:55458400-55460800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr2:55458400-55460800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:55458400-55460800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:55458400-55460800	Active TSS	Fetal Kidney	kidney
36	chr2:55458400-55460800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr2:55458400-55461400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:55458600-55460000	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr2:55458600-55460200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:55458600-55460200	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr2:55458600-55460400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:55458600-55460400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:55458600-55460400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:55458600-55460400	Active TSS	Muscle Satellite Cultured Cells	--
45	chr2:55458600-55460400	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr2:55458600-55460400	Active TSS	Colonic Mucosa	Colon
47	chr2:55458600-55460400	Active TSS	Hela-S3	cervix
48	chr2:55458600-55460400	Active TSS	NHEK	skin
49	chr2:55458600-55460600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr2:55458600-55460600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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