Variant report

Variant	rs7253677
Chromosome Location	chr19:18721790-18721791
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	HNF4G	chr19:18721075-18722070	HepG2	liver:	n/a	chr19:18722013-18722026 chr19:18721822-18721829 chr19:18722012-18722025 chr19:18722013-18722025 chr19:18721817-18721833 chr19:18722013-18722025 chr19:18721208-18721216 chr19:18722008-18722030 chr19:18721504-18721518 chr19:18722012-18722025
2	TEAD4	chr19:18721471-18721942	HepG2	liver:	n/a	n/a
3	MAZ	chr19:18721132-18721817	HepG2	liver:	n/a	chr19:18721650-18721660
4	ZBTB7A	chr19:18721308-18721930	HepG2	liver:	n/a	n/a
5	MYBL2	chr19:18721251-18721803	HepG2	liver:	n/a	n/a
6	NR3C1	chr19:18721517-18721844	ECC-1	luminal epithelium:	n/a	n/a
7	NFIC	chr19:18721251-18722067	HepG2	liver:	n/a	n/a
8	RXRA	chr19:18721114-18721968	HepG2	liver:	n/a	n/a
9	NR2F2	chr19:18720900-18722132	HepG2	liver:	n/a	chr19:18722014-18722029
10	EP300	chr19:18721351-18721929	HepG2	liver:	n/a	chr19:18721667-18721676 chr19:18721839-18721855
11	FOS	chr19:18721404-18721850	HUVEC	blood vessel:	n/a	chr19:18721575-18721586 chr19:18721738-18721747 chr19:18721653-18721662 chr19:18721654-18721663 chr19:18721652-18721661
12	ZBTB7A	chr19:18721174-18723265	ECC-1	luminal epithelium:	n/a	chr19:18722623-18722631
13	EP300	chr19:18721142-18723056	ECC-1	luminal epithelium:	n/a	chr19:18722743-18722759 chr19:18722567-18722583 chr19:18722742-18722758 chr19:18721667-18721676 chr19:18721839-18721855 chr19:18722746-18722762
14	FOXA1	chr19:18721381-18721810	HepG2	liver:	n/a	n/a
15	POLR2A	chr19:18719758-18723372	HepG2	liver:	n/a	n/a
16	REST	chr19:18721435-18721833	HepG2	liver:	n/a	n/a
17	JUND	chr19:18721737-18721934	H1-hESC	embryonic stem cell:	n/a	chr19:18721738-18721747
18	ELF1	chr19:18721093-18721961	HepG2	liver:	n/a	n/a
19	CEBPB	chr19:18721644-18721822	HepG2	liver:	n/a	n/a
20	TCF12	chr19:18721164-18723022	ECC-1	luminal epithelium:	n/a	chr19:18722354-18722361
21	ZBTB7A	chr19:18720992-18722058	HepG2	liver:	n/a	n/a
22	TCF7L2	chr19:18721337-18721865	HCT-116	colon:	n/a	n/a
23	HDAC2	chr19:18720987-18722019	HepG2	liver:	n/a	n/a
24	TEAD4	chr19:18721360-18722022	ECC-1	luminal epithelium:	n/a	n/a
25	MAX	chr19:18721371-18721931	ECC-1	luminal epithelium:	n/a	chr19:18721650-18721660
26	CEBPD	chr19:18721036-18722077	HepG2	liver:	n/a	n/a
27	TCF12	chr19:18721314-18721867	HepG2	liver:	n/a	n/a
28	NFIC	chr19:18721290-18722073	ECC-1	luminal epithelium:	n/a	n/a
29	CEBPD	chr19:18721426-18721882	HepG2	liver:	n/a	n/a
30	HNF4A	chr19:18721058-18721933	HepG2	liver:	n/a	chr19:18721822-18721829 chr19:18721817-18721833 chr19:18721208-18721216 chr19:18721504-18721518
31	RXRA	chr19:18721243-18721995	HepG2	liver:	n/a	n/a
32	YY1	chr19:18721132-18721999	HepG2	liver:	n/a	chr19:18721667-18721676 chr19:18721566-18721577 chr19:18721661-18721675 chr19:18721847-18721858 chr19:18721280-18721291
33	ELF1	chr19:18721403-18721880	HepG2	liver:	n/a	n/a
34	EP300	chr19:18720368-18722181	HepG2	liver:	n/a	chr19:18721667-18721676 chr19:18721839-18721855
35	POLR2A	chr19:18721508-18721812	HUVEC	blood vessel:	n/a	n/a
36	ZBTB7A	chr19:18721115-18724078	ECC-1	luminal epithelium:	n/a	chr19:18722623-18722631
37	SP1	chr19:18720956-18722007	HepG2	liver:	n/a	chr19:18721875-18721884 chr19:18721463-18721477 chr19:18721654-18721668 chr19:18721752-18721766 chr19:18721751-18721763 chr19:18721435-18721449
38	TEAD4	chr19:18721412-18721911	ECC-1	luminal epithelium:	n/a	n/a
39	TEAD4	chr19:18721527-18721919	H1-hESC	embryonic stem cell:	n/a	n/a
40	TCF12	chr19:18721193-18722490	ECC-1	luminal epithelium:	n/a	chr19:18722354-18722361
41	EP300	chr19:18721312-18722088	ECC-1	luminal epithelium:	n/a	chr19:18721667-18721676 chr19:18721839-18721855

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:18721740-18721790	LNCaP	prostate:	n/a
2	chr19:18721740-18721790	HNPCEpiC	eye:	n/a
3	chr19:18721740-18721790	ECC-1	luminal epithelium:	n/a
4	chr19:18721740-18721790	SK-N-SH_RA	brain:	n/a
5	chr19:18721740-18721790	NT2-D1	testis:	n/a
6	chr19:18721740-18721790	AG04450	lung:	fetal
7	chr19:18721740-18721790	GM12891	blood:	n/a
8	chr19:18721740-18721790	U87	brain:	n/a
9	chr19:18721740-18721790	IMR90	lung:	fetal
10	chr19:18721740-18721790	HEK293	kidney:	embryo
11	chr19:18721740-18721790	CMK	blood:	n/a
12	chr19:18721740-18721790	BE2_C	brain:	n/a
13	chr19:18721740-18721790	HCF	heart:	n/a
14	chr19:18721740-18721790	Caco-2	colon:	n/a
15	chr19:18721740-18721790	Jurkat	blood:	n/a
16	chr19:18721740-18721790	NHBE	bronchial:	n/a
17	chr19:18721740-18721790	AG09319	gingival:	n/a
18	chr19:18721740-18721790	ProgFib	skin:	n/a
19	chr19:18721740-18721790	NB4	blood:	n/a
20	chr19:18721740-18721790	Hela-S3	cervix:	n/a
21	chr19:18721740-18721790	GM19239	blood:	n/a
22	chr19:18721740-18721790	PFSK-1	brain:	n/a
23	chr19:18721740-18721790	HepG2	liver:	n/a
24	chr19:18721740-18721790	HRCEpiC	kidney:	n/a
25	chr19:18721740-18721790	HL-60	blood:	n/a
26	chr19:18721740-18721790	K562	blood:	n/a
27	chr19:18721740-18721790	HMEC	breast:	n/a
28	chr19:18721740-18721790	BJ	skin:	n/a
29	chr19:18721740-18721790	HRE	kidney:	n/a
30	chr19:18721740-18721790	HCPEpiC	choroid plexus:	n/a
31	chr19:18721740-18721790	MCF10A-Er-Src	breast:	n/a
32	chr19:18721740-18721790	SKMC	muscle:	n/a
33	chr19:18721740-18721790	HCT-116	colon:	n/a
34	chr19:18721740-18721790	SAEC	small airway:	n/a
35	chr19:18721740-18721790	AG04449	skin:	fetal
36	chr19:18721740-18721790	PrEC	prostate:	n/a
37	chr19:18721740-18721790	HEEpiC	esophagus:	n/a
38	chr19:18721740-18721790	RPTEC	kidney:	n/a
39	chr19:18721740-18721790	GM12878	blood:	n/a
40	chr19:18721740-18721790	HUVEC	blood vessel:	n/a
41	chr19:18721740-18721790	PANC-1	pancreas:	n/a
42	chr19:18721740-18721790	HCM	heart:	n/a
43	chr19:18721740-18721790	SK-N-MC	brain:	n/a
44	chr19:18721740-18721790	ovcar-3	ovarian:	n/a
45	chr19:18721740-18721790	AoSMC	blood vessel:	n/a
46	chr19:18721740-18721790	A549	lung:	n/a
47	chr19:18721740-18721790	MCF-7	breast:	n/a
48	chr19:18721740-18721790	SK-N-SH	brain:	n/a
49	chr19:18721740-18721790	GM12892	blood:	n/a
50	chr19:18721740-18721790	H1-hESC	embryonic stem cell:	embryo

No.	Distal block	Cell Line	Cell type
1	chr19:18720681..18723578-chr19:18792529..18794058,2	K562	blood:
2	chr19:18719600..18721808-chr19:18793150..18795640,2	MCF-7	breast:
3	chr19:18714423..18716001-chr19:18720923..18723094,2	K562	blood:
4	chr19:18715795..18719274-chr19:18719391..18724999,7	MCF-7	breast:
5	chr19:18714258..18716711-chr19:18719461..18722423,3	K562	blood:
6	chr19:18713204..18718867-chr19:18719015..18725496,7	MCF-7	breast:
7	chr19:18700084..18702080-chr19:18719094..18721979,3	K562	blood:

Variant related genes	Relation type
TMEM59L	TF binding region
CRLF1	TF binding region
TMEM59L	CpG island
CRLF1	CpG island
ENSG00000006016	Chromatin interaction
ENSG00000105696	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000105662	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12461284	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2002632	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2074177	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2238647	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2283617	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2314662	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3761031	0.97[ASN][1000 genomes]
rs4808140	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4808141	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4808828	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246833	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7249956	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7252535	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8109611	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs886243	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911287	chr19:18699333-18727913	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv911288	chr19:18700047-18739497	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv911291	chr19:18701499-18726856	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
12	nsv911292	chr19:18701499-18731658	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7253677	CRLF1	cis	Muscle Skeletal	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18718800-18721800	Weak transcription	Right Atrium	heart
2	chr19:18720600-18723000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:18720600-18723200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr19:18720600-18723200	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr19:18720800-18722800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:18721000-18722600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
7	chr19:18721000-18722600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:18721000-18722800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr19:18721000-18723000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:18721000-18723200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:18721000-18723600	Enhancers	Lung	lung
12	chr19:18721200-18722000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
13	chr19:18721200-18722000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
14	chr19:18721200-18722200	Enhancers	HSMM	muscle
15	chr19:18721200-18722400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
16	chr19:18721200-18723000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:18721200-18723000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
18	chr19:18721200-18723400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:18721200-18723400	Bivalent Enhancer	HUVEC	blood vessel
20	chr19:18721200-18724400	Bivalent Enhancer	Placenta	Placenta
21	chr19:18721400-18721800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr19:18721400-18721800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:18721400-18721800	Bivalent Enhancer	Spleen	Spleen
24	chr19:18721400-18721800	Active TSS	HepG2	liver
25	chr19:18721400-18722000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
26	chr19:18721400-18722000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr19:18721400-18722000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr19:18721400-18722000	Bivalent Enhancer	Left Ventricle	heart
29	chr19:18721400-18722200	Bivalent Enhancer	Brain Anterior Caudate	brain
30	chr19:18721400-18722600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:18721400-18722600	Bivalent Enhancer	NH-A	brain
32	chr19:18721400-18722800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr19:18721400-18723000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:18721400-18723000	Bivalent Enhancer	Fetal Stomach	stomach
35	chr19:18721400-18723200	Bivalent Enhancer	Adipose Nuclei	Adipose
36	chr19:18721400-18723200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr19:18721400-18723400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:18721400-18723400	Enhancers	Pancreas	Pancrea
39	chr19:18721400-18723600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
40	chr19:18721400-18723600	Bivalent Enhancer	Fetal Thymus	thymus
41	chr19:18721400-18723600	Bivalent Enhancer	HMEC	breast
42	chr19:18721400-18724200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr19:18721600-18721800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
44	chr19:18721600-18721800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
45	chr19:18721600-18721800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:18721600-18721800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
47	chr19:18721600-18722000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
48	chr19:18721600-18722000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:18721600-18722000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:18721600-18722000	Bivalent/Poised TSS	Thymus	Thymus

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