Variant report

Variant	rs13215804
Chromosome Location	chr6:28415572-28415573
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	MXI1	chr6:28413894-28415609	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ZSCAN23	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1005126	1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11751928	1.00[CHB][hapmap]
rs11752919	0.83[ASW][hapmap]
rs11755387	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs11756111	0.84[LWK][hapmap]
rs13190937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13193272	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13196606	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13199081	1.00[CHB][hapmap]
rs13203055	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13209596	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1474589	0.81[ASW][hapmap]
rs16894011	0.91[CHB][hapmap]
rs16894091	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16894106	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16894128	0.80[ASN][1000 genomes]
rs17856167	0.91[CHB][hapmap]
rs2021745	0.80[LWK][hapmap]
rs2071965	0.83[ASW][hapmap]
rs2232427	0.91[CHB][hapmap]
rs2531813	0.80[LWK][hapmap]
rs2859372	0.80[LWK][hapmap]
rs3799499	0.88[ASW][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3799500	1.00[CHB][hapmap]
rs3800328	0.94[ASW][hapmap]
rs4254981	0.88[ASW][hapmap]
rs58020991	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6899389	0.88[ASW][hapmap]
rs6902687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6905380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6922169	0.88[ASW][hapmap]
rs6928773	0.83[ASW][hapmap]
rs6931359	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6940744	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs71559081	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7740429	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7754960	1.00[CHB][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs7774981	0.88[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9468356	0.84[CHB][hapmap]
rs9468358	1.00[CHB][hapmap]
rs9468364	0.90[CHB][hapmap]
rs9969098	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs13215804	ZSCAN23	cis	Artery Tibial	GTEx
rs13215804	ZSCAN23	cis	cerebellum	SCAN
rs13215804	ZNF323	cis	parietal	SCAN
rs13215804	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs13215804	HLA-H	cis	multi-tissue	Pritchard
rs13215804	SLC17A1	cis	parietal	SCAN
rs13215804	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs13215804	ZNF192	cis	cerebellum	SCAN
rs13215804	HLA-A	cis	multi-tissue	Pritchard
rs13215804	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13215804	ZSCAN23	cis	parietal	SCAN
rs13215804	AL022393.7	cis	Muscle Skeletal	GTEx
rs13215804	ZSCAN23	cis	Heart Left Ventricle	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28414000-28415600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:28414400-28415600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:28414400-28415600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:28414400-28415600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:28414400-28415600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:28414400-28415600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:28414400-28415600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr6:28414600-28415600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:28414600-28415600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:28414600-28415600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
11	chr6:28415200-28415600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr6:28415200-28415600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:28415400-28415600	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr6:28415400-28415600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:28415400-28415600	Bivalent Enhancer	Primary T cells from cord blood	blood
16	chr6:28415400-28415600	Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr6:28415400-28415600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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