Variant report

Variant	rs10052929
Chromosome Location	chr5:80598005-80598006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:80596604-80598133	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr5:80596442-80598163	SK-N-SH	brain:	n/a	chr5:80597972-80597987
3	GABPA	chr5:80596916-80598063	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr5:80597089-80598049	K562	blood:	n/a	n/a
5	MXI1	chr5:80596595-80598086	IMR90	lung:	n/a	chr5:80597972-80597987
6	POLR2A	chr5:80596928-80598037	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:80596900-80598488	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr5:80596965-80598057	K562	blood:	n/a	n/a
9	POLR2A	chr5:80596859-80598018	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr5:80596887-80598034	K562	blood:	n/a	n/a
11	POLR2A	chr5:80596859-80598073	PFSK-1	brain:	n/a	n/a
12	YY1	chr5:80597111-80598052	GM12878	blood:	n/a	n/a
13	GABPA	chr5:80596616-80598136	MCF-7	breast:	n/a	n/a
14	MTA3	chr5:80596945-80598010	GM12878	blood:	n/a	n/a
15	REST	chr5:80596830-80598075	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr5:80596783-80598482	HepG2	liver:	n/a	n/a
17	POLR2A	chr5:80596958-80598791	PANC-1	pancreas:	n/a	n/a
18	HEY1	chr5:80597020-80598057	K562	blood:	n/a	n/a
19	HCFC1	chr5:80596463-80598024	Hela-S3	cervix:	n/a	n/a
20	GABPA	chr5:80596684-80598041	A549	lung:	n/a	n/a
21	CREB1	chr5:80596822-80598075	HepG2	liver:	n/a	n/a
22	POLR2A	chr5:80597074-80598192	GM19193	blood:	n/a	n/a
23	POLR2A	chr5:80596244-80598801	IMR90	lung:	n/a	n/a
24	MYC	chr5:80597066-80598317	K562	blood:	n/a	n/a

Variant related genes	Relation type
CKMT2-AS1	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10041138	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10061143	0.96[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10072332	0.81[ASN][1000 genomes]
rs1039326	0.92[JPT][hapmap]
rs12514420	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12516414	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs12519433	0.82[CEU][hapmap];0.89[YRI][hapmap]
rs1566433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16876403	0.85[CHB][hapmap]
rs17228569	0.85[CEU][hapmap]
rs2124888	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs2270824	0.85[CHB][hapmap]
rs2277037	0.85[CHB][hapmap]
rs2406557	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3756636	0.85[CEU][hapmap]
rs4502795	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4703828	0.85[CHB][hapmap]
rs4704711	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4704713	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4704714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4704717	0.85[CHB][hapmap]
rs56938600	0.82[ASN][1000 genomes]
rs57040652	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57266451	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6863732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6868743	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6868762	0.88[CEU][hapmap]
rs6871676	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6885028	0.82[CEU][hapmap]
rs6889795	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6896441	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6896890	0.82[ASN][1000 genomes]
rs7709071	0.82[CEU][hapmap]
rs7709149	0.82[CEU][hapmap]
rs7718501	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7731117	0.82[ASN][1000 genomes]
rs7734902	0.85[CEU][hapmap]
rs871701	0.83[JPT][hapmap]
rs955948	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10052929	ATP6AP1L	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80593800-80599800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:80595200-80598200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr5:80595200-80598200	Active TSS	Right Atrium	heart
4	chr5:80595200-80598600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr5:80595400-80598200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr5:80595400-80598200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr5:80595400-80598600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:80595400-80598800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr5:80595800-80598400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:80595800-80598400	Active TSS	Fetal Kidney	kidney
11	chr5:80595800-80598400	Active TSS	K562	blood
12	chr5:80596000-80598200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:80596000-80598400	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr5:80596000-80598400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr5:80596200-80598200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr5:80596200-80598200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr5:80596200-80598800	Active TSS	NHLF	lung
18	chr5:80596400-80598400	Active TSS	A549	lung
19	chr5:80596400-80598400	Active TSS	NHDF-Ad	bronchial
20	chr5:80596400-80598600	Active TSS	Aorta	Aorta
21	chr5:80596400-80598800	Active TSS	GM12878-XiMat	blood
22	chr5:80596600-80598200	Active TSS	H1 Cell Line	embryonic stem cell
23	chr5:80596600-80598200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:80596600-80598200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:80596600-80598200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:80596600-80598200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:80596600-80598200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:80596600-80598200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:80596600-80598200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:80596600-80598200	Active TSS	Fetal Intestine Large	intestine
31	chr5:80596600-80598200	Active TSS	Left Ventricle	heart
32	chr5:80596600-80598200	Active TSS	Pancreas	Pancrea
33	chr5:80596600-80598200	Active TSS	Hela-S3	cervix
34	chr5:80596600-80598200	Active TSS	HMEC	breast
35	chr5:80596600-80598200	Active TSS	HSMMtube	muscle
36	chr5:80596600-80598400	Active TSS	Muscle Satellite Cultured Cells	--
37	chr5:80596600-80598400	Active TSS	Psoas Muscle	Psoas
38	chr5:80596600-80598800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:80596800-80598200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:80596800-80598200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:80596800-80598200	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr5:80596800-80598200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:80596800-80598200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:80596800-80598200	Active TSS	Colon Smooth Muscle	Colon
45	chr5:80596800-80598200	Active TSS	Fetal Intestine Small	intestine
46	chr5:80596800-80598200	Active TSS	Gastric	stomach
47	chr5:80596800-80598200	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr5:80596800-80598200	Active TSS	Rectal Smooth Muscle	rectum
49	chr5:80596800-80598200	Active TSS	HSMM	muscle
50	chr5:80596800-80598200	Active TSS	HUVEC	blood vessel

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