Variant report

Variant	rs17153599
Chromosome Location	chr7:79847565-79847566
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:15)

rs_ID	r²[population]
rs13222403	0.91[GIH][hapmap];0.91[MEX][hapmap]
rs17153558	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs17153603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2714449	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs2714452	0.82[CEU][hapmap]
rs2714454	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs2714467	0.88[CEU][hapmap]
rs2886611	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3890739	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4458811	0.91[AFR][1000 genomes]
rs4610665	0.92[AFR][1000 genomes]
rs56284710	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56343702	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6954752	0.89[AFR][1000 genomes]
rs7800163	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429785	chr7:79589749-80177049	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1024312	chr7:79832637-80004812	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1029180	chr7:79832637-80017560	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17153599	PHTF2	cis	cerebellum	SCAN
rs17153599	CCDC146	cis	cerebellum	SCAN
rs17153599	DTX2	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79809600-79847600	Weak transcription	HUVEC	blood vessel
2	chr7:79815000-79848200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:79815000-79850200	Weak transcription	Lung	lung
4	chr7:79815200-79859600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:79816400-79854800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:79817000-79851200	Weak transcription	Aorta	Aorta
7	chr7:79820600-79853800	Weak transcription	Left Ventricle	heart
8	chr7:79825400-79856600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:79829200-79853000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:79830800-79848400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:79831000-79848200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:79831000-79853800	Weak transcription	Gastric	stomach
13	chr7:79831600-79850800	Weak transcription	Fetal Stomach	stomach
14	chr7:79831800-79861200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:79832400-79855000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:79834000-79850600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:79836000-79859600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:79836600-79861000	Weak transcription	HSMMtube	muscle
19	chr7:79837800-79847600	Strong transcription	Primary hematopoietic stem cells	blood
20	chr7:79838000-79849400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:79838800-79850400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:79839600-79850200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:79840000-79853800	Weak transcription	Brain Anterior Caudate	brain
24	chr7:79840200-79849400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:79840200-79850400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:79840400-79851600	Weak transcription	Small Intestine	intestine
27	chr7:79840800-79848000	Weak transcription	Hela-S3	cervix
28	chr7:79840800-79850400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:79841200-79853800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:79841200-79854000	Weak transcription	Fetal Intestine Small	intestine
31	chr7:79842800-79848200	Weak transcription	NH-A	brain
32	chr7:79842800-79853600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:79843000-79848200	Weak transcription	Brain Angular Gyrus	brain
34	chr7:79843000-79852600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:79843000-79862800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:79843400-79848200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr7:79843400-79850800	Weak transcription	Fetal Intestine Large	intestine
38	chr7:79843400-79853200	Weak transcription	Brain Substantia Nigra	brain
39	chr7:79843400-79853800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr7:79843600-79847800	Weak transcription	HSMM	muscle
41	chr7:79843800-79847600	Weak transcription	Placenta	Placenta
42	chr7:79843800-79853200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr7:79843800-79853600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:79844000-79849000	Enhancers	Dnd41	blood
45	chr7:79844200-79847600	Weak transcription	Osteobl	bone
46	chr7:79844200-79849600	Enhancers	Fetal Brain Male	brain
47	chr7:79844400-79853200	Weak transcription	Brain Germinal Matrix	brain
48	chr7:79844400-79853600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr7:79844600-79847800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr7:79845000-79847800	Enhancers	Primary T cells from cord blood	blood

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