Variant report

Variant	rs8068517
Chromosome Location	chr17:18095978-18095979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18093548..18096318-chr17:18098737..18101675,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1064629	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12449609	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12450483	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17806489	0.88[GIH][hapmap]
rs2056841	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2072652	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2072653	0.86[CEU][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2075659	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2124370	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2242595	0.93[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2272571	0.86[CEU][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2273026	0.88[GIH][hapmap]
rs2290507	0.91[GIH][hapmap]
rs2294914	0.88[GIH][hapmap]
rs3088175	0.84[GIH][hapmap]
rs4925145	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925147	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925157	0.88[GIH][hapmap]
rs57186648	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58804619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59179192	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827432	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8068517	SHMT1	cis	multi-tissue	Pritchard
rs8068517	LOC162632	cis	parietal	SCAN
rs8068517	SNORD49B	cis	cerebellum	SCAN
rs8068517	ALKBH5	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18090200-18103400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18090800-18098200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:18090800-18098400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:18090800-18104000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr17:18091000-18096000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr17:18091000-18096000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:18091200-18097000	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr17:18091200-18104600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr17:18091400-18097000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr17:18091400-18098800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:18091400-18114000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:18091600-18097800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:18091800-18098000	Weak transcription	Primary B cells from cord blood	blood
14	chr17:18091800-18098200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr17:18091800-18114400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:18092000-18096000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr17:18092000-18098000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:18092000-18104000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:18092200-18098000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr17:18092200-18098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr17:18092800-18096400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:18093000-18098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:18093200-18096000	Enhancers	Brain Angular Gyrus	brain
24	chr17:18093200-18096400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr17:18093400-18096000	Weak transcription	Aorta	Aorta
26	chr17:18093400-18097800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr17:18093400-18097800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr17:18093400-18098000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr17:18094200-18096400	Weak transcription	Hela-S3	cervix
30	chr17:18094200-18098200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:18094200-18114600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr17:18094400-18097800	Weak transcription	HMEC	breast
33	chr17:18094400-18098200	Weak transcription	Fetal Heart	heart
34	chr17:18094400-18114600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr17:18094600-18096000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr17:18094600-18114600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:18094800-18096000	Enhancers	Fetal Kidney	kidney
38	chr17:18094800-18096000	Enhancers	HepG2	liver
39	chr17:18094800-18096200	Weak transcription	Primary T cells from cord blood	blood
40	chr17:18094800-18096800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:18094800-18097800	Weak transcription	NHLF	lung
42	chr17:18094800-18098200	Weak transcription	Fetal Lung	lung
43	chr17:18094800-18098200	Weak transcription	HSMM	muscle
44	chr17:18094800-18098600	Weak transcription	HSMMtube	muscle
45	chr17:18094800-18098600	Weak transcription	NH-A	brain
46	chr17:18094800-18101800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr17:18094800-18103400	Strong transcription	Fetal Intestine Large	intestine
48	chr17:18095000-18096000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr17:18095000-18096600	Strong transcription	Primary B cells from peripheral blood	blood
50	chr17:18095000-18096800	Weak transcription	Primary monocytes fromperipheralblood	blood

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