Variant report

Variant	rs7727031
Chromosome Location	chr5:147255920-147255921
allele	C/T
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	POLR2A	chr5:147255691-147256063	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	chr5:147255871-147256007	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:147255764-147256063	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:147255398..147258341-chr5:147264911..147267895,3	MCF-7	breast:

Variant related genes	Relation type
SCGB3A2	TF binding region
ENSG00000251320	Chromatin interaction
ENSG00000248362	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1368408	0.81[TSI][hapmap]
rs1594667	0.87[TSI][hapmap]
rs17107349	0.88[ASN][1000 genomes]
rs17107379	0.82[LWK][hapmap];0.88[TSI][hapmap]
rs17107391	0.88[TSI][hapmap]
rs17703536	0.88[ASN][1000 genomes]
rs2400439	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3910183	0.82[LWK][hapmap];0.88[TSI][hapmap]
rs4551056	0.88[TSI][hapmap]
rs58925204	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60040551	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877478	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895894	1.00[ASN][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	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	nsv1028477	chr5:147255013-147416217	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 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	chr5:147254000-147256200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:147254600-147257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:147254800-147256000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:147254800-147256400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:147254800-147262200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:147255000-147256000	Enhancers	H9 Cell Line	embryonic stem cell
9	chr5:147255200-147256200	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr5:147255200-147256600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr5:147255200-147262000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:147255400-147256600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr5:147255400-147256600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr5:147255400-147257200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr5:147255400-147257800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:147255400-147258200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr5:147255400-147258400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr5:147255400-147259000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:147255400-147259800	Weak transcription	Fetal Heart	heart
20	chr5:147255800-147256800	Enhancers	Placenta Amnion	Placenta Amnion

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