Variant report

Variant	rs854767
Chromosome Location	chr17:18018263-18018264
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18005331..18008170-chr17:18017424..18019520,2	K562	blood:
2	chr17:18015610..18018849-chr17:18019499..18024205,4	MCF-7	breast:
3	chr17:18008952..18011744-chr17:18014672..18019225,4	MCF-7	breast:
4	chr17:18018156..18020480-chr17:18026722..18028730,2	K562	blood:

Variant related genes	Relation type
ENSG00000108591	Chromatin interaction
ENSG00000091536	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1008135	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1101727	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11078408	0.85[CEU][hapmap]
rs11078410	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11650021	0.81[EUR][1000 genomes]
rs11867241	0.87[EUR][1000 genomes]
rs11870660	0.85[CEU][hapmap]
rs12939020	0.81[EUR][1000 genomes]
rs2056842	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2955350	0.83[EUR][1000 genomes]
rs2955353	0.83[EUR][1000 genomes]
rs2955354	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955355	0.95[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs2955356	0.95[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs2955357	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955358	0.95[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs2955359	0.95[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs2955365	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955366	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955367	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2955368	0.84[EUR][1000 genomes]
rs2955370	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955372	0.95[CEU][hapmap];0.88[GIH][hapmap];0.84[EUR][1000 genomes]
rs2955377	0.90[CEU][hapmap];0.88[GIH][hapmap]
rs2955378	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs2955380	0.95[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs2955381	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs2955383	0.95[CEU][hapmap];0.88[GIH][hapmap];0.81[EUR][1000 genomes]
rs2955384	0.95[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs2955385	0.95[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs2974998	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2974999	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2975004	0.85[CHB][hapmap]
rs4072738	0.89[CEU][hapmap]
rs4072739	0.89[CEU][hapmap]
rs4299203	0.85[CEU][hapmap]
rs4365346	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4368210	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs4410135	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4426402	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4459604	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs4506967	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4506969	0.90[CEU][hapmap]
rs4561528	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4584886	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs4643387	0.83[EUR][1000 genomes]
rs4924832	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs4925135	0.83[EUR][1000 genomes]
rs4925136	0.82[EUR][1000 genomes]
rs59518074	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62073573	0.94[EUR][1000 genomes]
rs6502632	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs6502633	0.82[EUR][1000 genomes]
rs6502636	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6502637	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6826	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs712267	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712268	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7207461	0.83[EUR][1000 genomes]
rs7207821	0.95[CEU][hapmap]
rs7209003	0.95[CEU][hapmap]
rs7210400	0.83[EUR][1000 genomes]
rs7211714	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7212167	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs7212447	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs721669	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7219324	0.89[CEU][hapmap]
rs7224047	0.80[EUR][1000 genomes]
rs7406744	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7406982	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[EUR][1000 genomes]
rs741782	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7503738	0.80[EUR][1000 genomes]
rs8066764	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8068175	0.85[CEU][hapmap]
rs8075189	0.95[CEU][hapmap]
rs8080602	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs854763	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854768	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854770	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854789	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs854790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854792	0.84[EUR][1000 genomes]
rs854808	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854809	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854814	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854817	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854818	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9303144	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9894138	0.83[EUR][1000 genomes]
rs9896837	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs9897761	0.95[CEU][hapmap]
rs9899355	0.89[CEU][hapmap]
rs9913277	0.95[CEU][hapmap];0.88[GIH][hapmap]

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	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	nsv960429	chr17:17951047-18027679	Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv907769	chr17:18000321-18064195	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv457697	chr17:18003845-18046290	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv574527	chr17:18003845-18046290	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	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
12	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs854767	TOM1L2	cis	cerebellum	SCAN
rs854767	TOM1L2	cis	parietal	SCAN
rs854767	SREBF1	cis	Whole Blood	GTEx
rs854767	C17orf39	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18002400-18019600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr17:18003200-18021000	Weak transcription	Psoas Muscle	Psoas
3	chr17:18010600-18030400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:18010800-18020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr17:18011000-18022600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr17:18011200-18019400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:18011200-18022000	Weak transcription	Placenta	Placenta
8	chr17:18011200-18026200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:18014200-18018400	Enhancers	Liver	Liver
10	chr17:18014600-18022400	Weak transcription	Spleen	Spleen
11	chr17:18015400-18020400	Weak transcription	Fetal Muscle Leg	muscle
12	chr17:18015600-18018400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:18015600-18019000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr17:18015600-18019400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:18015600-18020800	Weak transcription	HSMMtube	muscle
16	chr17:18015600-18022000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr17:18015800-18019000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr17:18015800-18021000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr17:18017000-18020400	Enhancers	HepG2	liver
20	chr17:18017200-18019200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:18017400-18021000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:18018200-18018400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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