Variant report

Variant	rs17628870
Chromosome Location	chr7:70778579-70778580
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	POU5F1	chr7:70778454-70778895	H1-hESC	embryonic stem cell:	n/a	chr7:70778740-70778748 chr7:70778740-70778754 chr7:70778739-70778753 chr7:70778740-70778754 chr7:70778740-70778754

Variant related genes	Relation type
ENSG00000266688	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11760742	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11763372	0.86[EUR][1000 genomes]
rs11766837	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11768233	0.91[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs11770205	0.85[EUR][1000 genomes]
rs11771662	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13240200	0.91[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs1922526	0.90[GIH][hapmap]
rs2107795	0.83[EUR][1000 genomes]
rs2527313	0.83[EUR][1000 genomes]
rs2707425	0.91[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs2707433	0.91[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs2707438	0.82[EUR][1000 genomes]
rs34445434	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34822312	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35964468	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4717591	0.91[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55690472	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6972973	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6974603	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6976905	0.88[GIH][hapmap]
rs7790268	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7792219	0.86[EUR][1000 genomes]
rs7811093	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1015261	chr7:70404302-71255933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17628870	STAG3L4	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70765800-70790000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:70773400-70780800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr7:70773400-70789800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:70774000-70779800	Weak transcription	Fetal Stomach	stomach
5	chr7:70777000-70788800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:70777600-70779000	Enhancers	Colon Smooth Muscle	Colon
7	chr7:70778000-70779400	Enhancers	Rectal Smooth Muscle	rectum
8	chr7:70778200-70778800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr7:70778200-70778800	Enhancers	Brain Anterior Caudate	brain
10	chr7:70778200-70779200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr7:70778200-70779400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr7:70778200-70779400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr7:70778200-70779400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr7:70778200-70779600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:70778200-70779600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:70778400-70778800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:70778400-70778800	Enhancers	Fetal Muscle Leg	muscle
18	chr7:70778400-70779000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr7:70778400-70779000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr7:70778400-70779000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr7:70778400-70779000	Enhancers	Brain Germinal Matrix	brain
22	chr7:70778400-70779000	Enhancers	Fetal Lung	lung
23	chr7:70778400-70779200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:70778400-70779400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr7:70778400-70779400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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