Variant report

Variant	rs2643194
Chromosome Location	chr17:37853048-37853049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr17:37852303-37853193	H1-hESC	embryonic stem cell:	n/a	chr17:37852695-37852704 chr17:37852418-37852429
2	TEAD4	chr17:37851225-37853069	HepG2	liver:	n/a	n/a
3	MYBL2	chr17:37851089-37853120	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:37853032-37853082	NHDF-neo	bronchial:	n/a
2	chr17:37853032-37853082	HL-60	blood:	n/a
3	chr17:37853032-37853082	HCPEpiC	choroid plexus:	n/a
4	chr17:37853032-37853082	PrEC	prostate:	n/a
5	chr17:37853032-37853082	BE2_C	brain:	n/a
6	chr17:37853032-37853082	HAEpiC	amniotic membrane:	n/a
7	chr17:37853032-37853082	CMK	blood:	n/a
8	chr17:37853032-37853082	PFSK-1	brain:	n/a
9	chr17:37853032-37853082	HIPEpiC	eye:	n/a
10	chr17:37853032-37853082	SK-N-MC	brain:	n/a
11	chr17:37853032-37853082	SKMC	muscle:	n/a
12	chr17:37853032-37853082	HEEpiC	esophagus:	n/a
13	chr17:37853032-37853082	HCT-116	colon:	n/a
14	chr17:37853032-37853082	AoSMC	blood vessel:	n/a
15	chr17:37853032-37853082	GM12878	blood:	n/a
16	chr17:37853032-37853082	ovcar-3	ovarian:	n/a
17	chr17:37853032-37853082	ProgFib	skin:	n/a
18	chr17:37853032-37853082	SAEC	small airway:	n/a
19	chr17:37853032-37853082	RPTEC	kidney:	n/a
20	chr17:37853032-37853082	AG10803	skin:	n/a
21	chr17:37853032-37853082	GM12891	blood:	n/a
22	chr17:37853032-37853082	MCF10A-Er-Src	breast:	n/a
23	chr17:37853032-37853082	HRE	kidney:	n/a
24	chr17:37853032-37853082	NH-A	brain:	n/a
25	chr17:37853032-37853082	HUVEC	blood vessel:	n/a
26	chr17:37853032-37853082	HPAEpiC	pulmonary alveolar:	n/a
27	chr17:37853032-37853082	HMEC	breast:	n/a
28	chr17:37853032-37853082	Jurkat	blood:	n/a
29	chr17:37853032-37853082	HCF	heart:	n/a
30	chr17:37853032-37853082	MCF-7	breast:	n/a
31	chr17:37853032-37853082	Hepatocyte	liver:	n/a
32	chr17:37853032-37853082	GM19239	blood:	n/a
33	chr17:37853032-37853082	IMR90	lung:	fetal
34	chr17:37853032-37853082	GM06990	blood:	n/a
35	chr17:37853032-37853082	AG09319	gingival:	n/a
36	chr17:37853032-37853082	HNPCEpiC	eye:	n/a
37	chr17:37853032-37853082	NHBE	bronchial:	n/a
38	chr17:37853032-37853082	ECC-1	luminal epithelium:	n/a
39	chr17:37853032-37853082	Hela-S3	cervix:	n/a
40	chr17:37853032-37853082	BJ	skin:	n/a
41	chr17:37853032-37853082	A549	lung:	n/a
42	chr17:37853032-37853082	HCM	heart:	n/a
43	chr17:37853032-37853082	T-47D	breast:	n/a
44	chr17:37853032-37853082	PANC-1	pancreas:	n/a
45	chr17:37853032-37853082	AG09309	skin:	n/a
46	chr17:37853032-37853082	HEK293	kidney:	embryo
47	chr17:37853032-37853082	HRCEpiC	kidney:	n/a
48	chr17:37853032-37853082	GM12892	blood:	n/a
49	chr17:37853032-37853082	SK-N-SH	brain:	n/a
50	chr17:37853032-37853082	NT2-D1	testis:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37852050..37854882-chr17:37862447..37865325,2	K562	blood:

No data

Variant related genes	Relation type
ERBB2	TF binding region
ERBB2	CpG island
ENSG00000141736	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1058808	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11653998	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1565923	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1810132	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2088126	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517951	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643195	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904766	0.86[ASN][1000 genomes]
rs2934967	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2934971	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2941520	0.84[EUR][1000 genomes]
rs2952155	0.97[ASN][1000 genomes]
rs2952156	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2952157	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4252627	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs903506	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	esv1792029	chr17:37797757-37886460	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv528093	chr17:37814080-37866005	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv908214	chr17:37814224-37861833	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2643194	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs2643194	PGAP3	cis	Thyroid	GTEx
rs2643194	PGAP3	cis	Heart Left Ventricle	GTEx
rs2643194	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37845000-37856000	Weak transcription	Lung	lung
2	chr17:37845200-37854600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:37845200-37854600	Weak transcription	Brain Hippocampus Middle	brain
4	chr17:37845400-37854800	Weak transcription	Placenta	Placenta
5	chr17:37845400-37855000	Weak transcription	Brain Substantia Nigra	brain
6	chr17:37845400-37855400	Weak transcription	Left Ventricle	heart
7	chr17:37845400-37855800	Weak transcription	Aorta	Aorta
8	chr17:37845600-37853400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr17:37845600-37854600	Weak transcription	Primary B cells from cord blood	blood
10	chr17:37845600-37855000	Weak transcription	Fetal Brain Female	brain
11	chr17:37845600-37855400	Weak transcription	Colon Smooth Muscle	Colon
12	chr17:37845600-37855800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr17:37845600-37855800	Weak transcription	Ovary	ovary
14	chr17:37845600-37855800	Weak transcription	Psoas Muscle	Psoas
15	chr17:37845600-37855800	Weak transcription	Right Ventricle	heart
16	chr17:37845600-37855800	Weak transcription	HSMMtube	muscle
17	chr17:37845600-37856000	Weak transcription	Esophagus	oesophagus
18	chr17:37845600-37856000	Weak transcription	Spleen	Spleen
19	chr17:37845800-37854800	Weak transcription	Primary T cells from cord blood	blood
20	chr17:37845800-37854800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:37845800-37855600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr17:37845800-37855600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:37845800-37855600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:37845800-37855600	Weak transcription	NHEK	skin
25	chr17:37845800-37855800	Weak transcription	HSMM	muscle
26	chr17:37845800-37855800	Weak transcription	NHLF	lung
27	chr17:37845800-37858000	Weak transcription	K562	blood
28	chr17:37850200-37853200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr17:37850600-37853400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr17:37850600-37853600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr17:37850600-37854200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:37850800-37853200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr17:37850800-37853400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:37850800-37853400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr17:37850800-37853400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr17:37850800-37853400	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr17:37851000-37853400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr17:37851200-37853400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:37851600-37853400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr17:37851600-37853600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr17:37851600-37855600	Weak transcription	Fetal Stomach	stomach
42	chr17:37851800-37855600	Weak transcription	Fetal Lung	lung
43	chr17:37852000-37853400	Enhancers	Pancreas	Pancrea
44	chr17:37852000-37854800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr17:37852000-37855800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:37852000-37855800	Weak transcription	Brain Anterior Caudate	brain
47	chr17:37852200-37855600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr17:37852200-37855800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr17:37852200-37856000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr17:37852400-37853200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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