Variant report

Variant	rs10829133
Chromosome Location	chr10:18941670-18941671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:18939213-18942897	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:18939570..18941733-chr6:27856904..27858914,2	MCF-7	breast:
2	chr10:18938647..18942217-chr10:18945513..18950534,9	MCF-7	breast:
3	chr10:18937279..18942257-chr10:18944156..18951752,16	MCF-7	breast:
4	chr10:18940688..18942837-chr10:18963626..18966243,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARL5B-1	chr10:18941165-18942371	ENSG00000246675

No data

Variant related genes	Relation type
NSUN6	TF binding region
ENSG00000152487	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000165997	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10741099	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741100	0.83[EUR][1000 genomes]
rs10764542	0.85[ASN][1000 genomes]
rs10764566	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10764584	1.00[ASN][1000 genomes]
rs10828835	1.00[ASN][1000 genomes]
rs10828859	1.00[ASN][1000 genomes]
rs10828879	1.00[ASN][1000 genomes]
rs10828901	1.00[ASN][1000 genomes]
rs10828906	1.00[ASN][1000 genomes]
rs10829038	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829041	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10829042	0.82[EUR][1000 genomes]
rs10829139	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829140	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014830	1.00[ASN][1000 genomes]
rs11014852	1.00[ASN][1000 genomes]
rs11015243	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11015263	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015306	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11015307	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11015411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359508	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12412484	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12569760	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12570585	0.95[ASN][1000 genomes]
rs12765362	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771084	0.90[ASN][1000 genomes]
rs12772534	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12776325	0.85[ASN][1000 genomes]
rs12781038	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1352655	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880682	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1968961	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2691159	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4328135	0.91[ASN][1000 genomes]
rs4456162	0.85[AMR][1000 genomes]
rs4578284	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4747353	1.00[ASN][1000 genomes]
rs4748474	0.90[ASN][1000 genomes]
rs4748475	0.85[ASN][1000 genomes]
rs4748480	0.95[ASN][1000 genomes]
rs4748489	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4748491	0.83[AFR][1000 genomes]
rs4748495	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4748503	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4748508	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482516	1.00[ASN][1000 genomes]
rs6482529	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7068575	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7070695	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071192	1.00[ASN][1000 genomes]
rs7071897	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7073651	0.95[ASN][1000 genomes]
rs7075304	0.83[AFR][1000 genomes]
rs7077692	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7078884	0.90[ASN][1000 genomes]
rs7080903	1.00[ASN][1000 genomes]
rs7081811	1.00[ASN][1000 genomes]
rs7082094	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7084525	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085332	0.90[ASN][1000 genomes]
rs7085587	0.90[ASN][1000 genomes]
rs7086034	0.90[ASN][1000 genomes]
rs7086911	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7088214	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7090293	0.90[ASN][1000 genomes]
rs7091578	1.00[ASN][1000 genomes]
rs7095070	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098313	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099975	1.00[ASN][1000 genomes]
rs7101352	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7895235	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895709	0.84[AMR][1000 genomes]
rs7907153	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10829133	NSUN6	cis	Skin Sun Exposed Lower leg	GTEx
rs10829133	RP11-499P20.2	cis	lung	GTEx
rs10829133	NSUN6	cis	Adipose Subcutaneous	GTEx
rs10829133	NSUN6	cis	Nerve Tibial	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18941000-18943000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:18941000-18945800	Weak transcription	Left Ventricle	heart
3	chr10:18941000-18947200	Weak transcription	Pancreas	Pancrea
4	chr10:18941000-18947200	Weak transcription	Thymus	Thymus
5	chr10:18941000-18947400	Weak transcription	Gastric	stomach
6	chr10:18941200-18941800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr10:18941200-18942000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr10:18941200-18942400	Weak transcription	Fetal Intestine Small	intestine
9	chr10:18941200-18942600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr10:18941200-18942600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr10:18941200-18942600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:18941200-18943200	Weak transcription	Fetal Muscle Leg	muscle
13	chr10:18941200-18945000	Weak transcription	Fetal Lung	lung
14	chr10:18941200-18946600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr10:18941200-18946600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr10:18941200-18946800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr10:18941200-18946800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr10:18941200-18946800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr10:18941200-18946800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr10:18941200-18946800	Weak transcription	NH-A	brain
21	chr10:18941200-18946800	Weak transcription	NHLF	lung
22	chr10:18941200-18947000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:18941200-18947000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr10:18941200-18947000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr10:18941200-18947000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr10:18941200-18947000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr10:18941200-18947000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr10:18941200-18947000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr10:18941200-18947000	Weak transcription	Brain Anterior Caudate	brain
30	chr10:18941200-18947000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr10:18941200-18947000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr10:18941200-18947000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:18941200-18947000	Weak transcription	Brain Substantia Nigra	brain
34	chr10:18941200-18947000	Weak transcription	Fetal Brain Male	brain
35	chr10:18941200-18947000	Weak transcription	Fetal Stomach	stomach
36	chr10:18941200-18947000	Weak transcription	Psoas Muscle	Psoas
37	chr10:18941200-18947000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr10:18941200-18947000	Weak transcription	HMEC	breast
39	chr10:18941200-18947000	Weak transcription	NHEK	skin
40	chr10:18941200-18947200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr10:18941200-18947200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr10:18941200-18947200	Weak transcription	Fetal Thymus	thymus
43	chr10:18941200-18947200	Weak transcription	HUVEC	blood vessel
44	chr10:18941400-18941800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr10:18941400-18941800	Weak transcription	Primary T cells from cord blood	blood
46	chr10:18941400-18941800	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr10:18941400-18942600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr10:18941400-18942600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr10:18941400-18942800	Weak transcription	Fetal Intestine Large	intestine
50	chr10:18941400-18943000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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