Variant report

Variant	rs649039
Chromosome Location	chr18:11945481-11945482
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:11907394..11908966-chr18:11944115..11945998,2	MCF-7	breast:
2	chr18:11944456..11952400-chr18:11978684..11982486,15	K562	blood:
3	chr18:11943801..11947480-chr18:11981525..11984599,3	MCF-7	breast:
4	chr18:11945202..11946852-chr18:11982600..11984410,2	K562	blood:

Variant related genes	Relation type
ENSG00000154889	Chromatin interaction
ENSG00000141401	Chromatin interaction
ENSG00000273141	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs16976851	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1811452	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34478333	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34803006	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35932750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs581799	0.85[JPT][hapmap]
rs585176	0.85[JPT][hapmap];0.83[AMR][1000 genomes]
rs591880	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600405	0.83[AMR][1000 genomes]
rs604427	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604453	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs622863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629550	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630068	0.85[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs648676	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs649459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650958	0.83[AMR][1000 genomes]
rs651889	0.83[AMR][1000 genomes]
rs661885	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs662981	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs665149	0.83[AMR][1000 genomes]
rs665169	0.83[AMR][1000 genomes]
rs677254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs677359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679158	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs682249	0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs689390	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs694635	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7226885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7227036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7504853	0.83[AMR][1000 genomes]
rs8098140	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs9952563	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9956744	0.83[AMR][1000 genomes]
rs9962395	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS 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	66 gene(s)	inside rSNPs	diseases
3	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
7	nsv1063339	chr18:11909588-11979264	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv576495	chr18:11917410-11986557	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv909385	chr18:11938102-11986557	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
10	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs649039	RP11-820I16.1	cis	Nerve Tibial	GTEx
rs649039	RP11-820I16.1	cis	Thyroid	GTEx
rs649039	RP11-820I16.1	cis	Esophagus Muscularis	GTEx
rs649039	RP11-820I16.1	cis	Artery Tibial	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11927400-11946000	Weak transcription	Ovary	ovary
2	chr18:11927800-11946000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:11938000-11945600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr18:11938600-11946200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr18:11938600-11946400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr18:11939000-11947200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr18:11941600-11947400	Enhancers	Placenta	Placenta
8	chr18:11942200-11946200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr18:11942800-11945800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr18:11942800-11946400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr18:11942800-11947000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr18:11943400-11947000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr18:11943800-11946000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr18:11943800-11946000	Weak transcription	Pancreas	Pancrea
15	chr18:11943800-11946000	Weak transcription	A549	lung
16	chr18:11943800-11946200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr18:11943800-11946800	Weak transcription	Psoas Muscle	Psoas
18	chr18:11943800-11947600	Weak transcription	Gastric	stomach
19	chr18:11944400-11946000	Enhancers	Hela-S3	cervix
20	chr18:11944400-11946000	Weak transcription	K562	blood
21	chr18:11944600-11946600	Enhancers	NHEK	skin
22	chr18:11945000-11946000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr18:11945000-11946200	Weak transcription	Small Intestine	intestine
24	chr18:11945200-11945800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr18:11945200-11946000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr18:11945200-11946400	Weak transcription	HSMMtube	muscle
27	chr18:11945400-11945800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr18:11945400-11945800	Weak transcription	Colonic Mucosa	Colon
29	chr18:11945400-11945800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr18:11945400-11946000	Enhancers	HepG2	liver

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