Variant report

Variant	rs17589306
Chromosome Location	chr4:100368786-100368787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1573496	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17529509	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2119889	0.94[AMR][1000 genomes]
rs2165672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34925826	0.94[AMR][1000 genomes]
rs971074	1.00[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3355763	chr4:100070566-100376814	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1010988	chr4:100105463-100444445	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1000659	chr4:100117276-100444445	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3353320	chr4:100147870-100425701	Genic enhancers ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv3394995	chr4:100147890-100425671	Enhancers Genic enhancers Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv879660	chr4:100284199-100380148	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv1847619	chr4:100321443-100430924	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3584518	chr4:100322445-100377763	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv3584519	chr4:100323870-100477462	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	esv3584520	chr4:100324071-100400696	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17589306	SLC39A8	cis	cerebellum	SCAN
rs17589306	EMCN	cis	parietal	SCAN
rs17589306	TSPAN5	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100366200-100373400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:100367600-100369000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:100367800-100369000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:100367800-100369000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:100367800-100369000	Enhancers	HMEC	breast
6	chr4:100367800-100369000	Enhancers	HSMMtube	muscle
7	chr4:100367800-100369400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:100367800-100369400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:100367800-100369400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:100368000-100368800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:100368000-100369000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr4:100368000-100369000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr4:100368000-100369000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr4:100368000-100369000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:100368000-100369000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:100368000-100369200	Enhancers	Stomach Mucosa	stomach
17	chr4:100368000-100369400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr4:100368200-100368800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr4:100368200-100369000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:100368200-100369000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr4:100368200-100369000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:100368200-100369000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:100368200-100369000	Flanking Active TSS	A549	lung
24	chr4:100368400-100368800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr4:100368400-100368800	Enhancers	NH-A	brain
26	chr4:100368400-100369000	Enhancers	NHEK	skin
27	chr4:100368600-100369000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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