Variant report

Variant	rs2114039
Chromosome Location	chr4:55092626-55092627
allele	A/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	MXI1	chr4:55092563-55098831	IMR90	lung:	n/a	n/a
2	CHD1	chr4:55092095-55098811	IMR90	lung:	n/a	chr4:55095204-55095214 chr4:55097509-55097519 chr4:55092863-55092873
3	CTCF	chr4:55092500-55092650	HUVEC	blood vessel:	n/a	n/a
4	CTBP2	chr4:55091201-55094655	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr4:55092296-55096262	IMR90	lung:	n/a	n/a
6	CTCF	chr4:55092620-55092770	AG10803	skin:	n/a	n/a
7	CTCF	chr4:55092600-55092750	GM12871	blood:	n/a	n/a
8	TCF7L2	chr4:55092286-55092744	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr4:55092480-55092630	AG09319	gingival:	n/a	n/a
10	SIN3A	chr4:55091998-55092834	H1-hESC	embryonic stem cell:	n/a	chr4:55092363-55092371
11	POLR2A	chr4:55092512-55093595	ProgFib	skin:	n/a	n/a
12	SMC3	chr4:55092553-55098497	SK-N-SH	brain:	n/a	chr4:55094171-55094179 chr4:55098142-55098152
13	CTCF	chr4:55092520-55092670	HRE	kidney:	n/a	n/a
14	CHD2	chr4:55092518-55092655	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr4:55092560-55092710	SAEC	small airway:	n/a	n/a
16	CTCF	chr4:55092480-55092630	HEEpiC	esophagus:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54774486..54775433-chr4:55092049..55092635,3	MCF-7	breast:

Variant related genes	Relation type
PDGFRA	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13435164	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1800812	0.92[GIH][hapmap];0.92[MEX][hapmap]
rs28622224	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864504	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554162	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554163	0.86[GIH][hapmap]
rs6554164	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6554165	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6850748	0.92[GIH][hapmap];0.92[MEX][hapmap]
rs7668190	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677751	0.81[GIH][hapmap]
rs7678144	0.92[GIH][hapmap];0.88[MEX][hapmap]
rs7682912	0.92[GIH][hapmap];0.92[MEX][hapmap]

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	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Corneal curvature	21665993	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2114039	GSX2	cis	parietal	SCAN
rs2114039	KIAA1211	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55084600-55092800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:55091000-55093800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:55091200-55094600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
4	chr4:55091200-55099000	Bivalent/Poised TSS	Fetal Kidney	kidney
5	chr4:55091400-55092800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr4:55091400-55092800	Bivalent Enhancer	Placenta	Placenta
7	chr4:55091400-55093000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:55091400-55093200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr4:55091400-55093200	Flanking Active TSS	NHDF-Ad	bronchial
10	chr4:55091400-55094600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr4:55091400-55094600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
12	chr4:55091400-55095000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
13	chr4:55091400-55095200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr4:55091400-55096600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
15	chr4:55091600-55092800	Enhancers	Lung	lung
16	chr4:55091600-55093200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
17	chr4:55091600-55093400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:55091600-55093800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:55091600-55093800	Flanking Active TSS	Osteobl	bone
20	chr4:55091600-55094600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
21	chr4:55091600-55094800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
22	chr4:55091600-55095000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:55091800-55092800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
24	chr4:55091800-55092800	Enhancers	Spleen	Spleen
25	chr4:55091800-55093000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:55091800-55093000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
27	chr4:55091800-55093000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
28	chr4:55091800-55093600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
29	chr4:55091800-55094600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr4:55091800-55094600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr4:55091800-55094600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:55091800-55094600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:55091800-55094600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:55091800-55094600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr4:55091800-55094800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
36	chr4:55091800-55095400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr4:55092000-55092800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
38	chr4:55092000-55092800	Active TSS	Ovary	ovary
39	chr4:55092000-55093000	Active TSS	Right Atrium	heart
40	chr4:55092000-55093200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
41	chr4:55092000-55094400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
42	chr4:55092000-55094400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:55092000-55094600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:55092000-55094800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
45	chr4:55092000-55094800	Flanking Bivalent TSS/Enh	NHEK	skin
46	chr4:55092000-55096800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr4:55092000-55100800	Active TSS	Aorta	Aorta
48	chr4:55092200-55092800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
49	chr4:55092200-55092800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
50	chr4:55092200-55092800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet

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