Variant report

Variant	rs12117020
Chromosome Location	chr1:166824580-166824581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:166811620..166813696-chr1:166822338..166824892,2	MCF-7	breast:
2	chr1:166824297..166825261-chr9:71394587..71395125,2	NB4	blood:
3	chr1:166814024..166815540-chr1:166822572..166825052,2	MCF-7	breast:
4	chr1:166806074..166810870-chr1:166822490..166828264,6	K562	blood:
5	chr1:166824391..166826364-chr1:166843627..166845764,3	K562	blood:
6	chr1:166818097..166822012-chr1:166824205..166826339,3	K562	blood:
7	chr1:166824337..166827192-chr1:166832491..166834290,2	MCF-7	breast:
8	chr1:166808565..166810635-chr1:166823388..166825949,2	MCF-7	breast:
9	chr1:166810016..166811525-chr1:166822714..166824801,2	MCF-7	breast:
10	chr1:166821008..166822696-chr1:166823106..166825090,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000152382	Chromatin interaction
ENSG00000143157	Chromatin interaction
ENSG00000187866	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10800267	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10800268	0.88[EUR][1000 genomes]
rs10800269	0.88[ASW][hapmap];0.95[CEU][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10918586	0.95[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10918587	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12028246	0.85[EUR][1000 genomes]
rs12029327	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12029367	0.82[ASW][hapmap];0.95[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12032642	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12039764	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12122547	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1476348	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1476349	0.95[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1476350	0.82[ASW][hapmap];0.95[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17331024	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2013526	0.93[GIH][hapmap]
rs2014854	0.93[GIH][hapmap]
rs2075947	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2232521	0.97[EUR][1000 genomes]
rs2272793	0.82[ASW][hapmap];0.95[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2312238	0.91[GIH][hapmap]
rs35622400	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3738209	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3753910	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4657607	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4657614	0.93[GIH][hapmap]
rs61408535	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6675033	0.88[ASW][hapmap];0.95[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6675153	0.89[EUR][1000 genomes]
rs6675750	0.88[ASW][hapmap];0.95[CEU][hapmap];0.95[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6677387	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6691431	0.83[ASW][hapmap];0.95[CEU][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6718	0.90[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs742006	0.95[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7531189	0.95[CEU][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7543998	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs7548191	0.90[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs7552562	0.93[GIH][hapmap]
rs7554414	0.87[EUR][1000 genomes]
rs760537	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12117020	DUTP6	cis	Adipose Subcutaneous	GTEx
rs12117020	MAEL	cis	lymphoblastoid	seeQTL
rs12117020	DUTP6	cis	Muscle Skeletal	GTEx
rs12117020	DUTP6	cis	lung	GTEx
rs12117020	DUTP6	cis	Esophagus Muscularis	GTEx
rs12117020	DUTP6	cis	Artery Tibial	GTEx
rs12117020	ANKRD36BP1	cis	parietal	SCAN
rs12117020	MAEL	cis	parietal	SCAN
rs12117020	UHMK1	cis	cerebellum	SCAN
rs12117020	DUTP6	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166809600-166844400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:166810400-166828600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:166810600-166825600	Strong transcription	NHLF	lung
4	chr1:166810600-166828200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:166810600-166829000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:166810600-166829400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:166810600-166834800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:166810600-166838800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:166810800-166825000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:166810800-166827400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr1:166810800-166827800	Strong transcription	A549	lung
12	chr1:166810800-166828600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:166810800-166828800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:166810800-166828800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:166810800-166832400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:166810800-166834200	Strong transcription	Fetal Stomach	stomach
17	chr1:166810800-166835200	Strong transcription	K562	blood
18	chr1:166810800-166839200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:166810800-166839200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:166811000-166835600	Strong transcription	Primary B cells from cord blood	blood
21	chr1:166811200-166834600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:166811200-166839800	Strong transcription	Primary T cells from cord blood	blood
23	chr1:166811400-166827400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:166811400-166829800	Strong transcription	Primary hematopoietic stem cells	blood
25	chr1:166811600-166827400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:166811800-166838600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:166811800-166838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:166812000-166825000	Strong transcription	HepG2	liver
29	chr1:166812000-166838400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:166812000-166838800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:166812200-166838800	Strong transcription	Fetal Thymus	thymus
32	chr1:166812800-166828800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:166813000-166834200	Strong transcription	Hela-S3	cervix
34	chr1:166813200-166832000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:166813200-166834600	Strong transcription	Placenta	Placenta
36	chr1:166813200-166840600	Strong transcription	Dnd41	blood
37	chr1:166813400-166827200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:166813400-166838400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:166813600-166825000	Strong transcription	Esophagus	oesophagus
40	chr1:166813600-166827600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:166813600-166828000	Strong transcription	Liver	Liver
42	chr1:166813600-166838600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:166813600-166839200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:166813800-166830000	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:166813800-166838400	Strong transcription	Fetal Intestine Large	intestine
46	chr1:166814200-166825000	Strong transcription	Rectal Smooth Muscle	rectum
47	chr1:166814200-166825000	Strong transcription	HSMMtube	muscle
48	chr1:166814200-166825000	Strong transcription	HUVEC	blood vessel
49	chr1:166814200-166829200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:166814200-166834000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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