Variant report

Variant	rs2209880
Chromosome Location	chr13:93875303-93875304
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	STAT5A	chr13:93874665-93875346	K562	blood:	n/a	chr13:93874703-93874710
2	TBP	chr13:93874987-93875633	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:93873798..93875690-chr13:93879042..93881368,2	MCF-7	breast:
2	chr13:93874469..93877049-chr13:93887079..93889596,2	K562	blood:
3	chr13:93852509..93854417-chr13:93874503..93876110,2	K562	blood:

Variant related genes	Relation type
GPC6	TF binding region
ENSG00000183098	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1328366	0.86[GIH][hapmap]
rs1328370	1.00[ASW][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs17267523	0.82[GIH][hapmap];1.00[LWK][hapmap];0.80[TSI][hapmap]
rs17645969	0.84[CEU][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17645998	0.84[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs17702471	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004191	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4400921	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61963718	0.85[EUR][1000 genomes]
rs72633947	0.85[EUR][1000 genomes]
rs8181846	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561275	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9561276	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561281	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:93868800-93876800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr13:93869000-93875400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:93869000-93878200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr13:93870000-93876600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr13:93870400-93876600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr13:93870600-93875400	Weak transcription	HepG2	liver
7	chr13:93870600-93877000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr13:93871200-93876800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr13:93871200-93876800	Weak transcription	HMEC	breast
10	chr13:93871200-93877800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:93871200-93878400	Weak transcription	Fetal Brain Female	brain
12	chr13:93871400-93876800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:93872800-93875400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:93873800-93875600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr13:93874200-93876600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr13:93874200-93876800	Weak transcription	Fetal Intestine Large	intestine
17	chr13:93874800-93875600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr13:93874800-93876600	Weak transcription	Fetal Intestine Small	intestine
19	chr13:93874800-93878200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:93875000-93875600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr13:93875000-93875800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr13:93875000-93876000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr13:93875000-93876000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr13:93875000-93878200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr13:93875200-93875600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr13:93875200-93876000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:93875200-93876600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr13:93875200-93876600	Enhancers	HUES6 Cell Line	embryonic stem cell

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