Variant report

Variant	rs16873543
Chromosome Location	chr6:45577134-45577135
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:45575303..45577184-chr6:45677286..45680162,2	MCF-7	breast:
2	chr6:45566597..45569065-chr6:45577055..45579600,2	K562	blood:
3	chr6:45387446..45391966-chr6:45573986..45578620,7	MCF-7	breast:
4	chr6:45576031..45578499-chr6:45617077..45619180,2	MCF-7	breast:
5	chr6:45575296..45578545-chr6:45595416..45597740,3	MCF-7	breast:
6	chr6:45576668..45578877-chr6:45680174..45683422,3	MCF-7	breast:
7	chr6:45575650..45578473-chr6:45689555..45692241,2	MCF-7	breast:
8	chr6:45387362..45392710-chr6:45572193..45578571,10	MCF-7	breast:
9	chr6:45576012..45577453-chr6:45682215..45682831,4	MCF-7	breast:
10	chr6:45575229..45578385-chr6:45580116..45583808,5	MCF-7	breast:
11	chr6:45574169..45577727-chr6:45643786..45647502,3	MCF-7	breast:
12	chr6:45554176..45557433-chr6:45573679..45578604,5	MCF-7	breast:
13	chr6:45504338..45506736-chr6:45575272..45577741,2	MCF-7	breast:
14	chr6:45575640..45578537-chr6:45586483..45588913,2	K562	blood:
15	chr6:45576232..45577212-chr6:45682162..45682912,2	MCF-7	breast:
16	chr6:45344156..45346489-chr6:45575839..45577947,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124813	Chromatin interaction
ENSG00000271857	Chromatin interaction
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12528502	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12661124	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12663210	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12665637	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1491142	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16873550	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs16873554	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2020084	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56083876	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57939401	0.80[ASN][1000 genomes]
rs58939587	0.80[ASN][1000 genomes]
rs59074904	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60540355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458449	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6458450	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458453	0.82[ASN][1000 genomes]
rs6458454	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458455	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6899443	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6930188	0.83[ASN][1000 genomes]
rs6936365	0.82[ASN][1000 genomes]
rs6938247	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs6938489	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs713270	0.85[ASN][1000 genomes]
rs73457129	0.90[AFR][1000 genomes]
rs73738526	0.82[ASN][1000 genomes]
rs7742335	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7752183	0.80[ASN][1000 genomes]
rs7752200	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7758915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759415	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7760394	0.86[AFR][1000 genomes]
rs7764338	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7766534	0.80[ASN][1000 genomes]
rs7768962	0.80[ASN][1000 genomes]
rs9296462	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296463	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9463108	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472518	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9472521	0.80[ASN][1000 genomes]
rs9472524	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472530	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9472531	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9472534	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS 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
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16873543	SPATA20	trans	lymphoblastoid	seeQTL
rs16873543	ENPP4	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45563800-45586200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:45564200-45579200	Weak transcription	Fetal Kidney	kidney
3	chr6:45573600-45577800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:45574400-45578200	Enhancers	Dnd41	blood
5	chr6:45574400-45579600	Enhancers	Stomach Mucosa	stomach
6	chr6:45574600-45577400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:45574600-45577600	Enhancers	HMEC	breast
8	chr6:45574600-45578000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:45574800-45579400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:45575000-45577600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:45575000-45577800	Enhancers	HSMM	muscle
12	chr6:45575000-45578400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:45575200-45577600	Enhancers	HSMMtube	muscle
14	chr6:45575200-45577800	Enhancers	NHDF-Ad	bronchial
15	chr6:45575200-45578400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:45575400-45577600	Enhancers	NH-A	brain
17	chr6:45575400-45577800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:45575400-45577800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr6:45575400-45577800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr6:45575400-45578000	Enhancers	NHLF	lung
21	chr6:45575600-45577200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:45575800-45577200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:45575800-45577200	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr6:45575800-45577400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr6:45575800-45577800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:45576200-45577400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:45576200-45579600	Enhancers	Pancreas	Pancrea
28	chr6:45576400-45577400	Enhancers	Left Ventricle	heart
29	chr6:45576400-45577400	Enhancers	Lung	lung
30	chr6:45576400-45577800	Enhancers	Esophagus	oesophagus
31	chr6:45576400-45578800	Weak transcription	Fetal Intestine Large	intestine
32	chr6:45576400-45581000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:45576600-45577400	Enhancers	Psoas Muscle	Psoas
34	chr6:45576600-45577400	Enhancers	NHEK	skin
35	chr6:45576600-45578200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:45576600-45581400	Weak transcription	Small Intestine	intestine
37	chr6:45576800-45581200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:45576800-45585000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:45577000-45577800	Enhancers	Right Atrium	heart
40	chr6:45577000-45578400	Enhancers	Gastric	stomach
41	chr6:45577000-45578400	Enhancers	Hela-S3	cervix
42	chr6:45577000-45581200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:45577000-45581200	Weak transcription	Osteobl	bone

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