Variant report

Variant	rs8037054
Chromosome Location	chr15:59887101-59887102
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	TEAD4	chr15:59886495-59887182	A549	lung:	n/a	n/a
2	SIN3AK20	chr15:59886563-59887129	A549	lung:	n/a	n/a
3	POLR2A	chr15:59886715-59887192	HepG2	liver:	n/a	n/a
4	REST	chr15:59886394-59887206	A549	lung:	n/a	chr15:59886512-59886521
5	BCL3	chr15:59886506-59887541	A549	lung:	n/a	chr15:59886977-59886986 chr15:59886512-59886521
6	TCF12	chr15:59886353-59888398	A549	lung:	n/a	chr15:59887089-59887099
7	CREB1	chr15:59886682-59887155	A549	lung:	n/a	n/a
8	FOXA2	chr15:59886535-59887210	A549	lung:	n/a	n/a
9	NR3C1	chr15:59886530-59887197	A549	lung:	n/a	n/a
10	GABPA	chr15:59886568-59887115	A549	lung:	n/a	n/a
11	JUND	chr15:59886525-59887260	A549	lung:	n/a	chr15:59886709-59886720 chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886716
12	MYBL2	chr15:59886620-59887160	HepG2	liver:	n/a	n/a
13	ATF3	chr15:59886536-59887289	A549	lung:	n/a	n/a
14	FOSL2	chr15:59886302-59887391	A549	lung:	n/a	chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886716
15	FOXA2	chr15:59886346-59887115	A549	lung:	n/a	n/a
16	ELF1	chr15:59886632-59887175	A549	lung:	n/a	n/a
17	FOSL2	chr15:59886498-59887209	A549	lung:	n/a	chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886716
18	MAX	chr15:59886489-59888320	A549	lung:	n/a	chr15:59886710-59886719
19	USF1	chr15:59886569-59887136	A549	lung:	n/a	n/a
20	CEBPB	chr15:59886402-59887459	A549	lung:	n/a	n/a
21	EP300	chr15:59886370-59888218	A549	lung:	n/a	n/a
22	ZBTB33	chr15:59886640-59887183	A549	lung:	n/a	n/a
23	BCL3	chr15:59886516-59887297	A549	lung:	n/a	chr15:59886977-59886986
24	SP1	chr15:59886467-59888083	A549	lung:	n/a	n/a
25	NR3C1	chr15:59886608-59887127	A549	lung:	n/a	n/a
26	EP300	chr15:59886471-59888087	A549	lung:	n/a	n/a
27	GATA3	chr15:59886681-59887155	T-47D	breast:	n/a	chr15:59886709-59886718
28	SP1	chr15:59886313-59888215	A549	lung:	n/a	n/a
29	MAX	chr15:59886548-59887383	A549	lung:	n/a	chr15:59886710-59886719
30	GATA3	chr15:59886400-59888118	A549	lung:	n/a	chr15:59886709-59886718
31	ATF3	chr15:59886503-59887273	A549	lung:	n/a	n/a
32	JUND	chr15:59886483-59887154	A549	lung:	n/a	chr15:59886709-59886720 chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886716

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCNT3-2	chr15:59887074-59887113	NONHSAT044178

Variant related genes	Relation type
GCNT3	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10083653	0.85[EUR][1000 genomes]
rs10163153	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11071458	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11852448	0.90[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11852458	0.95[CHB][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11852547	0.90[YRI][hapmap]
rs12438840	0.92[EUR][1000 genomes]
rs12440292	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901058	0.86[EUR][1000 genomes]
rs12902622	0.88[CEU][hapmap]
rs1552033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1552034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17269684	0.88[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes]
rs34444281	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34642067	0.93[EUR][1000 genomes]
rs35461856	0.86[EUR][1000 genomes]
rs4597252	0.90[EUR][1000 genomes]
rs71480534	0.86[EUR][1000 genomes]
rs71480535	0.92[EUR][1000 genomes]
rs71480536	0.88[EUR][1000 genomes]
rs7169937	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7171752	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8036403	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer 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 target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv569606	chr15:59883809-59894636	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59882400-59891600	Weak transcription	Small Intestine	intestine
2	chr15:59883600-59887200	Weak transcription	Colonic Mucosa	Colon
3	chr15:59883800-59887400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:59885400-59887200	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr15:59885400-59887800	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr15:59885400-59888000	Enhancers	Duodenum Mucosa	Duodenum
7	chr15:59886000-59889400	Enhancers	Fetal Intestine Small	intestine
8	chr15:59886400-59887200	Enhancers	NHEK	skin
9	chr15:59886400-59887400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:59886400-59887600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:59886400-59887600	Enhancers	NH-A	brain
12	chr15:59886400-59888000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:59886400-59888200	Enhancers	Osteobl	bone
14	chr15:59886400-59888600	Flanking Active TSS	A549	lung
15	chr15:59886600-59887200	Enhancers	Hela-S3	cervix
16	chr15:59886600-59888200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr15:59886600-59889400	Enhancers	Stomach Mucosa	stomach
18	chr15:59886800-59887200	Enhancers	HMEC	breast
19	chr15:59886800-59887400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:59886800-59887400	Enhancers	NHLF	lung
21	chr15:59886800-59887600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:59886800-59887600	Enhancers	Esophagus	oesophagus
23	chr15:59886800-59888000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr15:59886800-59888200	Flanking Active TSS	HepG2	liver
25	chr15:59886800-59888600	Enhancers	Ovary	ovary
26	chr15:59886800-59888800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:59886800-59892800	Enhancers	Fetal Intestine Large	intestine
28	chr15:59887000-59887400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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