Variant report

Variant	rs1572945
Chromosome Location	chr1:58069523-58069524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10493231	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10736394	1.00[EUR][1000 genomes]
rs1361558	1.00[EUR][1000 genomes]
rs1404385	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1404386	1.00[EUR][1000 genomes]
rs1524721	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1524724	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1539055	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1935046	1.00[GIH][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes]
rs2030718	0.88[EUR][1000 genomes]
rs4912267	0.94[EUR][1000 genomes]
rs6587786	0.85[EUR][1000 genomes]
rs6674849	1.00[EUR][1000 genomes]
rs7546312	0.89[EUR][1000 genomes]
rs7556036	0.89[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	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1012555	chr1:57950355-58103389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv523574	chr1:58018103-58087789	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv871684	chr1:58021206-58096379	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1572945	VGLL4	trans	brain	seeQTL
rs1572945	ADAD2	trans	brain	seeQTL
rs1572945	FCER2	trans	brain	seeQTL
rs1572945	INHBA	trans	brain	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58063000-58069600	Weak transcription	Stomach Mucosa	stomach
2	chr1:58065800-58071600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr1:58066000-58077200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:58066000-58089000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:58066200-58069600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:58066400-58071000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:58066400-58089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:58066600-58074400	Weak transcription	Fetal Heart	heart
9	chr1:58067000-58070800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:58067400-58070200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr1:58067600-58071200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:58068000-58069800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:58069000-58069800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:58069000-58070000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:58069200-58069600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:58069200-58069800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:58069200-58069800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:58069200-58070000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:58069400-58069600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
20	chr1:58069400-58069800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:58069400-58070000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr1:58069400-58070200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr1:58069400-58072000	Enhancers	H9 Cell Line	embryonic stem cell

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