Variant report

Variant	rs1855275
Chromosome Location	chr13:93874770-93874771
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	UBTF	chr13:93874690-93874878	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: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1413066	0.84[AFR][1000 genomes]
rs1413067	0.84[AFR][1000 genomes]
rs16948474	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1760330	0.84[AFR][1000 genomes]
rs1810933	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1855274	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs223307	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2388917	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2780374	0.87[AFR][1000 genomes]
rs2780381	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2780382	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2781035	0.84[AFR][1000 genomes]
rs2781051	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2781052	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs319517	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs319518	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs319520	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs319521	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320070	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320071	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320072	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs320075	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320076	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320078	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320079	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320080	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320081	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs364631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs366378	0.86[AFR][1000 genomes]
rs367924	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs368555	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs371381	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs372160	0.84[AFR][1000 genomes]
rs374389	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs376830	0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs376851	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs380416	0.84[AFR][1000 genomes]
rs380786	0.84[AFR][1000 genomes]
rs381662	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs385054	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs387992	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs389587	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs390904	0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs394973	0.84[AFR][1000 genomes]
rs397442	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs415326	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs417537	0.80[YRI][hapmap];0.84[AFR][1000 genomes]
rs417815	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs418948	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs420913	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs421861	0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs425257	0.84[AFR][1000 genomes]
rs425955	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs426342	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs426397	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs426787	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs427399	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs427409	0.84[AFR][1000 genomes]
rs427503	0.84[AFR][1000 genomes]
rs428015	0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs4300492	0.82[AFR][1000 genomes]
rs431476	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs432632	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs432800	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs433129	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs433135	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs437435	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs437703	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs437913	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs438139	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs439216	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs443603	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs444365	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs448518	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs450509	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs450732	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs451048	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs454092	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs475566	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs489911	0.80[YRI][hapmap];0.84[AFR][1000 genomes]
rs489934	0.84[AFR][1000 genomes]
rs521884	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs549385	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7330458	0.84[AFR][1000 genomes]
rs914865	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs914866	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv832682	chr13:93700861-93874801	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	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
4	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:27 , 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	chr13:93869200-93875200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:93870000-93876600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:93870400-93874800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:93870400-93876600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr13:93870600-93875400	Weak transcription	HepG2	liver
9	chr13:93870600-93877000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr13:93871000-93875000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr13:93871200-93876800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr13:93871200-93876800	Weak transcription	HMEC	breast
13	chr13:93871200-93877800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr13:93871200-93878400	Weak transcription	Fetal Brain Female	brain
15	chr13:93871400-93875000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr13:93871400-93876800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr13:93872800-93874800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:93872800-93875000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr13:93872800-93875000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr13:93872800-93875400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:93873000-93874800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr13:93873000-93875000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr13:93873000-93875200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr13:93873800-93875600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr13:93874000-93875200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr13:93874200-93876600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr13:93874200-93876800	Weak transcription	Fetal Intestine Large	intestine

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