Variant report

Variant	rs2025130
Chromosome Location	chr14:55118795-55118796
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	TCF12	chr14:55118721-55119477	ECC-1	luminal epithelium:	n/a	n/a
2	GATA3	chr14:55118631-55119573	A549	lung:	n/a	chr14:55118794-55118805
3	BCL3	chr14:55118760-55119375	A549	lung:	n/a	n/a
4	TEAD4	chr14:55118776-55119384	H1-hESC	embryonic stem cell:	n/a	chr14:55119123-55119132
5	EP300	chr14:55118358-55119458	T-47D	breast:	n/a	n/a
6	FOSL1	chr14:55118783-55119459	HCT-116	colon:	n/a	n/a
7	JUND	chr14:55118638-55119513	SK-N-SH	brain:	n/a	n/a
8	JUN	chr14:55118795-55119797	HUVEC	blood vessel:	n/a	n/a
9	TCF12	chr14:55118719-55119846	A549	lung:	n/a	chr14:55119526-55119533
10	GATA3	chr14:55118340-55119603	SK-N-SH	brain:	n/a	chr14:55118794-55118805
11	JUND	chr14:55118706-55119519	HCT-116	colon:	n/a	n/a
12	CEBPB	chr14:55118326-55119363	Hela-S3	cervix:	n/a	n/a
13	FOSL1	chr14:55118710-55119530	HCT-116	colon:	n/a	n/a
14	NFIC	chr14:55118774-55119863	SK-N-SH	brain:	n/a	n/a
15	MAX	chr14:55118740-55119409	A549	lung:	n/a	chr14:55119284-55119292
16	EP300	chr14:55118705-55119408	A549	lung:	n/a	n/a
17	TEAD4	chr14:55118760-55119346	ECC-1	luminal epithelium:	n/a	chr14:55119123-55119132
18	STAT3	chr14:55118371-55119385	MCF10A-Er-Src	breast:	n/a	n/a
19	TEAD4	chr14:55118733-55119408	HepG2	liver:	n/a	chr14:55119123-55119132
20	GATA3	chr14:55118753-55119317	T-47D	breast:	n/a	chr14:55118794-55118805
21	JUND	chr14:55118751-55119494	HCT-116	colon:	n/a	n/a
22	REST	chr14:55118698-55119354	A549	lung:	n/a	chr14:55119185-55119195
23	PBX3	chr14:55118653-55119546	SK-N-SH	brain:	n/a	n/a
24	STAT3	chr14:55118739-55119223	MCF10A-Er-Src	breast:	n/a	n/a
25	GATA3	chr14:55118238-55119702	SK-N-SH	brain:	n/a	chr14:55118794-55118805
26	FOSL2	chr14:55118655-55119454	A549	lung:	n/a	n/a
27	TCF12	chr14:55118751-55119475	ECC-1	luminal epithelium:	n/a	n/a
28	STAT3	chr14:55118520-55119255	Hela-S3	cervix:	n/a	n/a
29	FOXM1	chr14:55118736-55119579	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr14:55118753-55119507	U87	brain:	n/a	n/a
31	RAD21	chr14:55118760-55119547	IMR90	lung:	n/a	n/a
32	EP300	chr14:55118579-55119536	SK-N-SH	brain:	n/a	n/a
33	FOSL2	chr14:55118739-55119476	SK-N-SH	brain:	n/a	n/a
34	EP300	chr14:55118678-55119371	A549	lung:	n/a	n/a
35	POLR2A	chr14:55118604-55119997	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr14:55118766-55119389	MCF10A-Er-Src	breast:	n/a	n/a
37	SP1	chr14:55118601-55119471	A549	lung:	n/a	chr14:55119180-55119191 chr14:55119181-55119190 chr14:55119182-55119191 chr14:55119182-55119191
38	PRDM1	chr14:55118760-55119167	Hela-S3	cervix:	n/a	chr14:55118987-55119000
39	SP1	chr14:55118646-55119530	HCT-116	colon:	n/a	chr14:55119180-55119191 chr14:55119181-55119190 chr14:55119182-55119191 chr14:55119182-55119191
40	SIN3AK20	chr14:55118755-55119342	HCT-116	colon:	n/a	n/a
41	JUND	chr14:55118690-55119417	H1-hESC	embryonic stem cell:	n/a	n/a
42	TEAD4	chr14:55118760-55119381	HCT-116	colon:	n/a	chr14:55119123-55119132
43	JUND	chr14:55118605-55119498	T-47D	breast:	n/a	n/a
44	TCF12	chr14:55118600-55119756	SK-N-SH	brain:	n/a	chr14:55119526-55119533
45	JUND	chr14:55118660-55119765	SK-N-SH	brain:	n/a	n/a
46	FOS	chr14:55118375-55119316	MCF10A-Er-Src	breast:	n/a	n/a
47	TEAD4	chr14:55118689-55119472	A549	lung:	n/a	chr14:55119123-55119132
48	NFIC	chr14:55118710-55119761	ECC-1	luminal epithelium:	n/a	n/a
49	TEAD4	chr14:55118656-55119509	SK-N-SH	brain:	n/a	chr14:55119123-55119132
50	EP300	chr14:55118724-55119439	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:55032662..55034220-chr14:55117546..55119356,2	MCF-7	breast:
2	chr14:55085013..55087133-chr14:55116843..55119397,2	K562	blood:
3	chr14:55031461..55035668-chr14:55117629..55122192,5	MCF-7	breast:

Variant related genes	Relation type
SAMD4A	TF binding region
ENSG00000020577	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11158019	0.80[ASN][1000 genomes]
rs12586646	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12586705	0.84[ASN][1000 genomes]
rs12888372	0.81[CEU][hapmap];0.87[ASN][1000 genomes]
rs12890352	0.85[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs17728293	0.85[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap]
rs2358887	0.84[EUR][1000 genomes]
rs35399674	0.81[ASN][1000 genomes]
rs4553503	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4898844	0.85[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7142955	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7151563	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7155089	0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7158091	0.85[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs8011374	0.96[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs8022597	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs911621	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv974464	chr14:55092217-55152792	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2025130	GNPNAT1	cis	parietal	SCAN
rs2025130	PTGER2	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55107600-55121400	Weak transcription	Pancreas	Pancrea
2	chr14:55109600-55121400	Weak transcription	Spleen	Spleen
3	chr14:55109800-55119400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr14:55110800-55119600	Weak transcription	Lung	lung
5	chr14:55113200-55122000	Enhancers	Fetal Heart	heart
6	chr14:55114800-55118800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr14:55114800-55118800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:55114800-55120200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr14:55116000-55119400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr14:55116000-55121400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:55116200-55118800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr14:55116200-55122000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr14:55116400-55119600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:55116600-55118800	Enhancers	Stomach Smooth Muscle	stomach
15	chr14:55116600-55119000	Flanking Active TSS	A549	lung
16	chr14:55116600-55121600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr14:55116800-55119800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr14:55116800-55120000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr14:55117000-55118800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr14:55117000-55119000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr14:55117000-55119200	Enhancers	Fetal Muscle Leg	muscle
22	chr14:55117000-55119400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr14:55117000-55120000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:55117000-55121000	Enhancers	H9 Cell Line	embryonic stem cell
25	chr14:55117000-55121600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr14:55117000-55121600	Enhancers	Placenta	Placenta
27	chr14:55117200-55119000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr14:55117200-55119800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr14:55117200-55120000	Enhancers	Fetal Stomach	stomach
30	chr14:55117200-55121600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr14:55117400-55118800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr14:55117400-55119000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr14:55117400-55119400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr14:55117600-55118800	Enhancers	Rectal Smooth Muscle	rectum
35	chr14:55117600-55118800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr14:55117600-55119200	Weak transcription	Ovary	ovary
37	chr14:55117600-55119400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr14:55117600-55119400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr14:55117600-55119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr14:55117600-55119800	Enhancers	Liver	Liver
41	chr14:55117600-55121800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr14:55117600-55129400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr14:55117800-55119400	Weak transcription	Left Ventricle	heart
44	chr14:55117800-55120400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr14:55117800-55120400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr14:55118000-55118800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr14:55118000-55118800	Weak transcription	Aorta	Aorta
48	chr14:55118000-55118800	Enhancers	Colon Smooth Muscle	Colon
49	chr14:55118000-55119400	Enhancers	Hela-S3	cervix
50	chr14:55118000-55120000	Enhancers	Fetal Intestine Small	intestine

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