Variant report

Variant	rs1778544
Chromosome Location	chr1:247453161-247453162
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr1:247452376-247453277	K562	blood:	n/a	n/a
2	CBX3	chr1:247452267-247453590	K562	blood:	n/a	n/a
3	POLR2A	chr1:247452850-247453231	K562	blood:	n/a	n/a
4	TEAD4	chr1:247452462-247453253	K562	blood:	n/a	n/a
5	TRIM28	chr1:247452322-247453276	K562	blood:	n/a	n/a
6	TEAD4	chr1:247452434-247453255	K562	blood:	n/a	n/a
7	GATA2	chr1:247452484-247453213	K562	blood:	n/a	n/a
8	NR2F2	chr1:247452835-247453226	K562	blood:	n/a	n/a
9	TAL1	chr1:247452512-247453258	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:247453113-247453163	LNCaP	prostate:	n/a
2	chr1:247453113-247453163	HCF	heart:	n/a
3	chr1:247453113-247453163	NT2-D1	testis:	n/a
4	chr1:247453113-247453163	NHBE	bronchial:	n/a
5	chr1:247453113-247453163	HAEpiC	amniotic membrane:	n/a
6	chr1:247453113-247453163	Hela-S3	cervix:	n/a
7	chr1:247453113-247453163	MCF-7	breast:	n/a
8	chr1:247453113-247453163	ECC-1	luminal epithelium:	n/a
9	chr1:247453113-247453163	HCPEpiC	choroid plexus:	n/a
10	chr1:247453113-247453163	HPAEpiC	pulmonary alveolar:	n/a
11	chr1:247453113-247453163	CMK	blood:	n/a
12	chr1:247453113-247453163	GM12891	blood:	n/a
13	chr1:247453113-247453163	Hepatocyte	liver:	n/a
14	chr1:247453113-247453163	SKMC	muscle:	n/a
15	chr1:247453113-247453163	GM06990	blood:	n/a
16	chr1:247453113-247453163	HepG2	liver:	n/a
17	chr1:247453113-247453163	IMR90	lung:	fetal
18	chr1:247453113-247453163	HNPCEpiC	eye:	n/a
19	chr1:247453113-247453163	MCF10A-Er-Src	breast:	n/a
20	chr1:247453113-247453163	HIPEpiC	eye:	n/a
21	chr1:247453113-247453163	GM12878	blood:	n/a
22	chr1:247453113-247453163	HEK293	kidney:	embryo
23	chr1:247453113-247453163	K562	blood:	n/a
24	chr1:247453113-247453163	SAEC	small airway:	n/a
25	chr1:247453113-247453163	BJ	skin:	n/a
26	chr1:247453113-247453163	ProgFib	skin:	n/a
27	chr1:247453113-247453163	HUVEC	blood vessel:	n/a
28	chr1:247453113-247453163	SK-N-SH_RA	brain:	n/a
29	chr1:247453113-247453163	AG04449	skin:	fetal
30	chr1:247453113-247453163	RPTEC	kidney:	n/a
31	chr1:247453113-247453163	PFSK-1	brain:	n/a
32	chr1:247453113-247453163	ovcar-3	ovarian:	n/a
33	chr1:247453113-247453163	SK-N-MC	brain:	n/a
34	chr1:247453113-247453163	HRE	kidney:	n/a
35	chr1:247453113-247453163	Jurkat	blood:	n/a
36	chr1:247453113-247453163	HRPEpiC	eye:	n/a
37	chr1:247453113-247453163	NH-A	brain:	n/a
38	chr1:247453113-247453163	AG10803	skin:	n/a
39	chr1:247453113-247453163	U87	brain:	n/a
40	chr1:247453113-247453163	A549	lung:	n/a
41	chr1:247453113-247453163	Caco-2	colon:	n/a
42	chr1:247453113-247453163	AG09319	gingival:	n/a
43	chr1:247453113-247453163	AoSMC	blood vessel:	n/a
44	chr1:247453113-247453163	SK-N-SH	brain:	n/a
45	chr1:247453113-247453163	HCT-116	colon:	n/a
46	chr1:247453113-247453163	PrEC	prostate:	n/a
47	chr1:247453113-247453163	AG04450	lung:	fetal
48	chr1:247453113-247453163	HMEC	breast:	n/a
49	chr1:247453113-247453163	NB4	blood:	n/a
50	chr1:247453113-247453163	BE2_C	brain:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247450622..247452470-chr1:247452673..247454513,2	MCF-7	breast:
2	chr1:247453061..247455721-chr1:247491943..247494376,2	K562	blood:
3	chr1:247452284..247453974-chr1:247456330..247458629,2	K562	blood:
4	chr1:247444095..247447712-chr1:247449743..247453881,5	K562	blood:
5	chr1:247450966..247454008-chr1:247495973..247498678,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000202079	TF binding region
ENSG00000202079	CpG island
ENSG00000162714	Chromatin interaction
ENSG00000202079	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10754542	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10754544	0.83[EUR][1000 genomes]
rs10924983	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10924985	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10924989	0.85[ASN][1000 genomes]
rs11578583	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1192830	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1192831	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1192832	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12035515	0.84[ASN][1000 genomes]
rs1204493	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1341173	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1616299	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1771929	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1771943	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771948	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778546	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778549	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2153631	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2799540	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3850824	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4320815	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925532	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925533	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925534	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925615	0.98[ASN][1000 genomes]
rs4925621	0.82[ASN][1000 genomes]
rs56037169	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56399534	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674425	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6692645	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74163745	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7418221	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7528202	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540329	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552292	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs875883	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426180	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426181	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9426182	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9426233	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9725334	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1778544	ZNF496	cis	lung	GTEx
rs1778544	ZNF496	cis	Esophagus Muscularis	GTEx
rs1778544	ZNF496	cis	Nerve Tibial	GTEx
rs1778544	ZNF496	cis	Thyroid	GTEx
rs1778544	EDIL3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247436800-247457000	Weak transcription	HSMMtube	muscle
2	chr1:247445600-247455400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:247449200-247462000	Weak transcription	Primary T cells from cord blood	blood
4	chr1:247449400-247460800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:247449600-247462400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:247450400-247455200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:247450600-247454400	Weak transcription	Thymus	Thymus
8	chr1:247451000-247460800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:247451600-247460400	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:247452400-247455600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:247452400-247460800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:247452600-247454200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:247452600-247460800	Weak transcription	Brain Germinal Matrix	brain
14	chr1:247452600-247461200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:247452800-247454800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:247452800-247455000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:247452800-247455200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:247452800-247455400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:247452800-247455600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:247452800-247462000	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:247453000-247454600	Weak transcription	K562	blood
22	chr1:247453000-247454800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:247453000-247455000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:247453000-247455200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:247453000-247456200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:247453000-247460800	Weak transcription	Fetal Brain Female	brain
27	chr1:247453000-247462000	Weak transcription	Brain Inferior Temporal Lobe	brain

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