Variant report

Variant	rs10829148
Chromosome Location	chr10:18947476-18947477
allele	G/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	MAX	chr10:18947237-18948983	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:18946909-18949092	HepG2	liver:	n/a	n/a
3	POLR2A	chr10:18947134-18949376	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:18947127-18948557	HepG2	liver:	n/a	n/a
5	MYC	chr10:18947099-18949129	K562	blood:	n/a	n/a
6	TAF1	chr10:18947334-18947571	GM12891	blood:	n/a	n/a
7	CHD1	chr10:18946998-18949474	GM12878	blood:	n/a	chr10:18948546-18948556 chr10:18948735-18948745
8	RELA	chr10:18947087-18949047	GM19099	blood:	n/a	n/a
9	POLR2A	chr10:18946975-18949205	GM12892	blood:	n/a	n/a
10	MTA3	chr10:18947040-18948556	GM12878	blood:	n/a	n/a
11	ATF2	chr10:18947147-18947624	GM12878	blood:	n/a	n/a
12	POLR2A	chr10:18946806-18949630	K562	blood:	n/a	n/a
13	POLR2A	chr10:18947104-18949176	Raji	blood:	n/a	n/a
14	HEY1	chr10:18946926-18948691	HepG2	liver:	n/a	chr10:18948481-18948496 chr10:18948627-18948642
15	PML	chr10:18947412-18948530	K562	blood:	n/a	n/a
16	RELA	chr10:18947224-18949363	GM10847	blood:	n/a	n/a
17	POLR2A	chr10:18947000-18949749	MCF10A-Er-Src	breast:	n/a	n/a
18	EP300	chr10:18946944-18948489	K562	blood:	n/a	n/a
19	POLR2A	chr10:18947128-18949076	GM12892	blood:	n/a	n/a
20	POLR2A	chr10:18946935-18948599	HepG2	liver:	n/a	n/a
21	POLR2A	chr10:18947171-18948664	HepG2	liver:	n/a	n/a
22	SMC3	chr10:18947191-18947585	GM12878	blood:	n/a	n/a
23	BACH1	chr10:18947114-18947523	K562	blood:	n/a	n/a
24	MAZ	chr10:18946981-18949576	IMR90	lung:	n/a	n/a
25	POLR2A	chr10:18947209-18947779	HepG2	liver:	n/a	n/a
26	ZNF143	chr10:18947337-18949135	GM12878	blood:	n/a	chr10:18948511-18948521
27	RUNX3	chr10:18947250-18948644	GM12878	blood:	n/a	n/a
28	WRNIP1	chr10:18947116-18948522	GM12878	blood:	n/a	n/a
29	JUN	chr10:18947195-18948361	K562	blood:	n/a	chr10:18948266-18948275
30	POLR2A	chr10:18947451-18948743	U87	brain:	n/a	n/a
31	POLR2A	chr10:18947130-18949424	GM12892	blood:	n/a	n/a
32	RCOR1	chr10:18947124-18947605	GM12878	blood:	n/a	n/a
33	TBP	chr10:18947157-18949072	K562	blood:	n/a	n/a
34	EP300	chr10:18947026-18947478	GM12878	blood:	n/a	n/a
35	POLR2A	chr10:18947391-18947689	ProgFib	skin:	n/a	n/a
36	POLR2A	chr10:18947187-18949014	GM12878	blood:	n/a	n/a
37	POLR2A	chr10:18946812-18949486	GM12878	blood:	n/a	n/a
38	POLR2A	chr10:18947436-18949050	K562	blood:	n/a	n/a
39	POLR2A	chr10:18947004-18949484	HepG2	liver:	n/a	n/a
40	POLR2A	chr10:18947070-18949689	HepG2	liver:	n/a	n/a
41	CHD1	chr10:18946884-18951792	IMR90	lung:	n/a	chr10:18948546-18948556 chr10:18948735-18948745
42	POLR2A	chr10:18947001-18949088	K562	blood:	n/a	n/a
43	GABPA	chr10:18947399-18948674	MCF-7	breast:	n/a	n/a
44	POLR2A	chr10:18947149-18949112	GM18951	blood:	n/a	n/a
45	POLR2A	chr10:18947150-18949036	K562	blood:	n/a	n/a
46	TBL1XR1	chr10:18947001-18949387	GM12878	blood:	n/a	n/a
47	POLR2A	chr10:18947189-18949132	Hela-S3	cervix:	n/a	n/a
48	HEY1	chr10:18947099-18948663	HepG2	liver:	n/a	chr10:18948481-18948496 chr10:18948627-18948642
49	POLR2A	chr10:18947066-18949117	K562	blood:	n/a	n/a
50	MAFF	chr10:18947268-18947773	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:18938647..18942217-chr10:18945513..18950534,9	MCF-7	breast:
2	chr10:17271770..17274197-chr10:18946668..18948974,2	K562	blood:
3	chr10:18937279..18942257-chr10:18944156..18951752,16	MCF-7	breast:

Variant related genes	Relation type
ARL5B	TF binding region
ENSG00000271786	TF binding region
ENSG00000241058	Chromatin interaction
ENSG00000229124	Chromatin interaction
ENSG00000026025	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1055116	0.90[EUR][1000 genomes]
rs10734063	0.84[EUR][1000 genomes]
rs10741115	0.87[EUR][1000 genomes]
rs10741129	0.90[EUR][1000 genomes]
rs10741132	0.87[EUR][1000 genomes]
rs10764600	0.82[EUR][1000 genomes]
rs10764640	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10764691	0.89[EUR][1000 genomes]
rs10828965	0.82[EUR][1000 genomes]
rs10828975	0.82[EUR][1000 genomes]
rs10829022	0.86[EUR][1000 genomes]
rs10829037	0.87[EUR][1000 genomes]
rs10829039	0.87[EUR][1000 genomes]
rs10829058	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10829060	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10829070	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10829151	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10829213	0.89[EUR][1000 genomes]
rs11014892	0.82[EUR][1000 genomes]
rs11015048	0.81[EUR][1000 genomes]
rs11015196	0.86[EUR][1000 genomes]
rs11015255	0.81[EUR][1000 genomes]
rs11015312	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11015421	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11525266	0.82[EUR][1000 genomes]
rs12219183	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12359758	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3740102	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4748488	0.83[EUR][1000 genomes]
rs4748492	0.83[EUR][1000 genomes]
rs4748509	0.87[EUR][1000 genomes]
rs57066269	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57579336	0.83[EUR][1000 genomes]
rs62636218	0.83[EUR][1000 genomes]
rs6482533	0.83[EUR][1000 genomes]
rs6482597	0.90[EUR][1000 genomes]
rs7077722	0.83[EUR][1000 genomes]
rs7079325	0.83[EUR][1000 genomes]
rs7081690	0.90[EUR][1000 genomes]
rs7081977	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7087030	0.89[EUR][1000 genomes]
rs7099260	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7894016	0.83[EUR][1000 genomes]
rs7898781	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7899017	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7909570	0.88[EUR][1000 genomes]
rs7909845	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10829148	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs10829148	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10829148	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs10829148	RP11-499P20.2	cis	Thyroid	GTEx
rs10829148	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs10829148	RP11-499P20.2	cis	lung	GTEx
rs10829148	RP11-499P20.2	cis	Whole Blood	GTEx
rs10829148	ARL5B	cis	multi-tissue	Pritchard
rs10829148	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs10829148	ARL5B	cis	Whole Blood	GTEx
rs10829148	RP11-499P20.2	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18946600-18948400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr10:18946800-18947800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr10:18946800-18947800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr10:18946800-18949400	Active TSS	Liver	Liver
5	chr10:18946800-18949600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:18946800-18949600	Active TSS	Aorta	Aorta
7	chr10:18946800-18949600	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr10:18946800-18949800	Active TSS	Fetal Intestine Small	intestine
9	chr10:18946800-18949800	Active TSS	NHDF-Ad	bronchial
10	chr10:18946800-18950600	Active TSS	GM12878-XiMat	blood
11	chr10:18947000-18947600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:18947000-18947600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr10:18947000-18947600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr10:18947000-18947600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr10:18947000-18947600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr10:18947000-18947600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr10:18947000-18947600	Flanking Active TSS	Brain Angular Gyrus	brain
18	chr10:18947000-18947600	Flanking Active TSS	Brain Substantia Nigra	brain
19	chr10:18947000-18947600	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr10:18947000-18947600	Flanking Active TSS	Fetal Heart	heart
21	chr10:18947000-18947600	Flanking Active TSS	Fetal Lung	lung
22	chr10:18947000-18947600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr10:18947000-18947600	Enhancers	Small Intestine	intestine
24	chr10:18947000-18947600	Flanking Active TSS	HMEC	breast
25	chr10:18947000-18947600	Flanking Active TSS	NHEK	skin
26	chr10:18947000-18947800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr10:18947000-18947800	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr10:18947000-18947800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr10:18947000-18947800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:18947000-18947800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:18947000-18947800	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr10:18947000-18947800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr10:18947000-18947800	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr10:18947000-18947800	Flanking Active TSS	Dnd41	blood
35	chr10:18947000-18947800	Flanking Active TSS	NHLF	lung
36	chr10:18947000-18948000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr10:18947000-18948000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:18947000-18948000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr10:18947000-18948000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr10:18947000-18948000	Flanking Active TSS	NH-A	brain
41	chr10:18947000-18948000	Flanking Active TSS	Osteobl	bone
42	chr10:18947000-18949600	Active TSS	Stomach Mucosa	stomach
43	chr10:18947000-18949800	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr10:18947000-18949800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr10:18947000-18949800	Active TSS	Fetal Intestine Large	intestine
46	chr10:18947000-18949800	Active TSS	Psoas Muscle	Psoas
47	chr10:18947000-18949800	Active TSS	Right Atrium	heart
48	chr10:18947000-18950000	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr10:18947000-18950000	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr10:18947000-18950200	Active TSS	Colonic Mucosa	Colon

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