Variant report

Variant	rs17171367
Chromosome Location	chr7:38503389-38503390
allele	C/T
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	FOS	chr7:38503280-38503530	MCF10A-Er-Src	breast:	n/a	chr7:38503426-38503436 chr7:38503426-38503436
2	IRF1	chr7:38502965-38503544	K562	blood:	n/a	chr7:38503282-38503292 chr7:38503356-38503370 chr7:38503352-38503365 chr7:38503124-38503135 chr7:38503351-38503371 chr7:38503124-38503137 chr7:38503349-38503366 chr7:38503123-38503143 chr7:38503124-38503138 chr7:38503125-38503135 chr7:38503355-38503369 chr7:38503352-38503365 chr7:38503352-38503365 chr7:38503356-38503370 chr7:38503352-38503365 chr7:38503119-38503136 chr7:38503352-38503366 chr7:38503125-38503139
3	MAFK	chr7:38503276-38503472	IMR90	lung:	n/a	chr7:38503419-38503433 chr7:38503420-38503436
4	FOS	chr7:38503251-38503570	MCF10A-Er-Src	breast:	n/a	chr7:38503426-38503436 chr7:38503426-38503436
5	STAT2	chr7:38503178-38503627	K562	blood:	n/a	chr7:38503355-38503370 chr7:38503262-38503269
6	FOS	chr7:38503263-38503571	MCF10A-Er-Src	breast:	n/a	chr7:38503426-38503436 chr7:38503426-38503436
7	STAT3	chr7:38503364-38503458	MCF10A-Er-Src	breast:	n/a	n/a
8	NFIC	chr7:38503199-38503597	SK-N-SH	brain:	n/a	chr7:38503386-38503403
9	FOS	chr7:38503262-38503566	MCF10A-Er-Src	breast:	n/a	chr7:38503426-38503436 chr7:38503426-38503436

Variant related genes	Relation type
AMPH	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10951558	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12154302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1558617	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17171359	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17171377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171384	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17171387	0.84[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs17498899	1.00[CEU][hapmap]
rs17499670	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs17506922	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1861239	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2299949	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2893561	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs34057414	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3735089	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778876	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs3778879	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778882	1.00[CEU][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3778887	0.83[JPT][hapmap]
rs3807413	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3807416	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs3807419	0.91[ASN][1000 genomes]
rs3807425	0.87[JPT][hapmap]
rs3823594	0.90[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3823598	0.82[JPT][hapmap]
rs3943706	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs41279585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6953928	0.82[JPT][hapmap]
rs6956760	0.93[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1025974	chr7:38227528-38503472	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv538819	chr7:38227528-38503472	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv1020990	chr7:38257707-38503472	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv1031936	chr7:38319437-38503472	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv830965	chr7:38350614-38521047	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv1825425	chr7:38457144-38507180	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17171367	AMPH	cis	Nerve Tibial	GTEx
rs17171367	AMPH	cis	Skin Sun Exposed Lower leg	GTEx
rs17171367	AMPH	cis	normal skin	skin_eQTL
rs17171367	AMPH	cis	Adipose Subcutaneous	GTEx
rs17171367	AMPH	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38499400-38506800	Weak transcription	Left Ventricle	heart
2	chr7:38499800-38523600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:38501000-38522400	Weak transcription	Fetal Muscle Leg	muscle
4	chr7:38501600-38503800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:38501800-38522600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:38502000-38512200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:38502600-38503600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr7:38502600-38503600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr7:38502600-38503800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:38502600-38503800	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr7:38502600-38503800	Enhancers	Dnd41	blood
12	chr7:38502600-38504000	Enhancers	Brain Angular Gyrus	brain
13	chr7:38502600-38549400	Weak transcription	Fetal Stomach	stomach
14	chr7:38502800-38503600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:38502800-38503600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr7:38502800-38503600	Active TSS	Monocytes-CD14+_RO01746	blood
17	chr7:38502800-38503800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:38502800-38533800	Weak transcription	Aorta	Aorta
19	chr7:38503000-38503400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:38503000-38503400	Active TSS	Primary T cells fromperipheralblood	blood
21	chr7:38503000-38503400	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr7:38503000-38503400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:38503000-38503400	Enhancers	Brain Hippocampus Middle	brain
24	chr7:38503000-38503400	Active TSS	Duodenum Mucosa	Duodenum
25	chr7:38503200-38503400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:38503200-38503400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr7:38503200-38503400	Enhancers	Brain Anterior Caudate	brain
28	chr7:38503200-38503400	Enhancers	Fetal Lung	lung
29	chr7:38503200-38503400	Enhancers	GM12878-XiMat	blood
30	chr7:38503200-38503600	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr7:38503200-38503800	Enhancers	NHLF	lung
32	chr7:38503200-38504000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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