Variant report

Variant	rs8077577
Chromosome Location	chr17:18064730-18064731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18061892..18063958-chr17:18064455..18066875,2	MCF-7	breast:
2	chr17:18061742..18067292-chr17:18083221..18089651,7	K562	blood:
3	chr17:18063606..18070028-chr17:18081885..18087934,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266677	Chromatin interaction
ENSG00000091542	Chromatin interaction
ENSG00000091536	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10048161	0.94[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10451244	0.90[EUR][1000 genomes]
rs11078411	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11078412	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11652964	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11653988	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11654146	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11654177	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11654741	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11655588	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11655731	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11655797	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11656035	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11657194	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11658477	0.94[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11868832	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11868886	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11869582	0.81[CEU][hapmap]
rs11871039	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11871491	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12449313	0.94[GIH][hapmap]
rs12600694	0.88[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13284	0.83[CEU][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1563371	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1563373	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16960980	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16960983	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16960986	0.88[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16960990	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16960996	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16961153	0.94[GIH][hapmap]
rs2015336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2071242	0.90[GIH][hapmap]
rs2290502	0.90[GIH][hapmap]
rs2290503	0.90[GIH][hapmap]
rs2294913	0.94[GIH][hapmap]
rs28364628	0.90[GIH][hapmap]
rs28811342	0.90[EUR][1000 genomes]
rs3088233	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34474249	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36058389	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3817992	0.94[GIH][hapmap]
rs3829956	0.94[GIH][hapmap]
rs55918833	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58441148	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59354912	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60285171	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62072464	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62072465	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62072466	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62072467	0.89[EUR][1000 genomes]
rs62072468	0.88[EUR][1000 genomes]
rs62072496	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62072497	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62072498	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62072500	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62073602	0.93[EUR][1000 genomes]
rs62073603	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62073604	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62073605	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62073606	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62073607	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62073608	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62073609	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62073611	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62073615	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62073649	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62073650	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6502640	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7207276	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7215678	0.90[GIH][hapmap]
rs735960	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7498	0.90[GIH][hapmap]
rs8065026	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes]
rs8069094	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9909104	1.00[GIH][hapmap]
rs9913139	0.90[GIH][hapmap]
rs9916193	0.93[EUR][1000 genomes]
rs997315	0.94[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][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

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs8077577	EPN2	cis	parietal	SCAN
rs8077577	TRPV2	cis	cerebellum	SCAN
rs8077577	LOC162632	cis	parietal	SCAN
rs8077577	LOC162632	cis	cerebellum	SCAN
rs8077577	SHMT1	cis	cerebellum	SCAN
rs8077577	FLII	cis	cerebellum	SCAN
rs8077577	PLD6	cis	cerebellum	SCAN
rs8077577	SLC47A1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18062000-18064800	Weak transcription	Brain Anterior Caudate	brain
2	chr17:18062000-18065800	Enhancers	HSMM	muscle
3	chr17:18062000-18085600	Weak transcription	Brain Angular Gyrus	brain
4	chr17:18062200-18065200	Enhancers	Fetal Muscle Leg	muscle
5	chr17:18062200-18065400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr17:18062200-18066600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr17:18062200-18067600	Enhancers	K562	blood
8	chr17:18062200-18085000	Weak transcription	Right Atrium	heart
9	chr17:18062400-18066000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr17:18062400-18066000	Enhancers	GM12878-XiMat	blood
11	chr17:18062400-18066600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr17:18062600-18065400	Weak transcription	Spleen	Spleen
13	chr17:18062600-18070000	Weak transcription	Ovary	ovary
14	chr17:18063000-18064800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr17:18063000-18065200	Enhancers	HSMMtube	muscle
16	chr17:18063400-18065400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr17:18063400-18066400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:18063400-18066400	Weak transcription	Fetal Intestine Large	intestine
19	chr17:18063400-18066400	Weak transcription	Fetal Intestine Small	intestine
20	chr17:18063400-18066600	Weak transcription	Placenta	Placenta
21	chr17:18063600-18064800	Weak transcription	Osteobl	bone
22	chr17:18064200-18065000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr17:18064200-18065600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr17:18064200-18065800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr17:18064400-18064800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr17:18064400-18065800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr17:18064400-18066000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr17:18064600-18064800	Enhancers	Fetal Stomach	stomach
29	chr17:18064600-18065400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:18064600-18065600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr17:18064600-18065600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr17:18064600-18065600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr17:18064600-18065800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr17:18064600-18066000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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