Variant report

Variant	rs28838279
Chromosome Location	chr5:147249220-147249221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:147248505-147250221	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:147246099-147256428	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:147247774-147250258	H1-hESC	embryonic stem cell:	n/a	n/a
4	ATF2	chr5:147248499-147249707	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP4	chr5:147248553-147249415	H1-hESC	embryonic stem cell:	n/a	n/a
6	GATA3	chr5:147248847-147249479	MCF-7	breast:	n/a	n/a
7	GATA3	chr5:147248973-147249371	MCF-7	breast:	n/a	n/a
8	POLR2A	chr5:147248706-147250088	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr5:147248513-147250098	H1-hESC	embryonic stem cell:	n/a	n/a
10	CHD2	chr5:147248581-147249237	H1-hESC	embryonic stem cell:	n/a	n/a
11	CHD1	chr5:147248482-147249422	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr5:147248515-147249237	H1-hESC	embryonic stem cell:	n/a	n/a
13	TAF7	chr5:147248491-147249590	H1-hESC	embryonic stem cell:	n/a	n/a
14	GATA3	chr5:147248947-147249536	MCF-7	breast:	n/a	n/a
15	TBP	chr5:147248586-147249284	H1-hESC	embryonic stem cell:	n/a	n/a

No data

Variant related genes	Relation type
SCGB3A2	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11956228	0.80[EUR][1000 genomes]
rs12332164	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17625543	0.80[EUR][1000 genomes]
rs17703848	0.80[EUR][1000 genomes]
rs28792438	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28858457	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28895401	0.82[AMR][1000 genomes]
rs58022905	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59985420	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3334831	chr5:147165950-147339765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv933308	chr5:147173804-147269006	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3397747	chr5:147245959-147250557	Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv3321795	chr5:147247359-147251957	Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28838279	SCGB3A2	cis	Nerve Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147234200-147262400	Weak transcription	Right Atrium	heart
2	chr5:147247600-147260200	Weak transcription	Aorta	Aorta
3	chr5:147248600-147249400	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
4	chr5:147248600-147249400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:147248600-147249400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:147248600-147249400	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr5:147248800-147249400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:147248800-147249400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
9	chr5:147248800-147249400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
10	chr5:147248800-147249400	Transcr. at gene 5' and 3'	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:147248800-147249400	Enhancers	Brain Germinal Matrix	brain
12	chr5:147248800-147249600	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
13	chr5:147248800-147249600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
14	chr5:147248800-147249600	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
15	chr5:147248800-147252000	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
16	chr5:147248800-147253200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
17	chr5:147249000-147249400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
18	chr5:147249000-147254400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:147249200-147249400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:147249200-147249600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:147249200-147255800	Weak transcription	Placenta Amnion	Placenta Amnion

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