Variant report

Variant	rs10829140
Chromosome Location	chr10:18945606-18945607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18938647..18942217-chr10:18945513..18950534,9	MCF-7	breast:
2	chr10:18937279..18942257-chr10:18944156..18951752,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241058	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10741099	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741100	0.81[EUR][1000 genomes]
rs10764542	0.85[ASN][1000 genomes]
rs10764566	0.80[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	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829041	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10829133	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829139	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014830	1.00[ASN][1000 genomes]
rs11014852	1.00[ASN][1000 genomes]
rs11015243	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11015263	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015306	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11015307	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11015411	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359508	1.00[ASN][1000 genomes]
rs12412484	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12569760	0.84[AMR][1000 genomes]
rs12570585	0.95[ASN][1000 genomes]
rs12765362	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771084	0.90[ASN][1000 genomes]
rs12772534	1.00[ASN][1000 genomes]
rs12776325	0.85[ASN][1000 genomes]
rs12781038	1.00[ASN][1000 genomes]
rs1352655	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880682	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1968961	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2691159	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4328135	0.91[ASN][1000 genomes]
rs4456162	0.83[AMR][1000 genomes]
rs4578284	0.85[AFR][1000 genomes];0.84[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	1.00[ASN][1000 genomes]
rs4748495	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4748503	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4748508	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482516	1.00[ASN][1000 genomes]
rs6482529	1.00[ASN][1000 genomes]
rs7068575	0.95[ASN][1000 genomes]
rs7070695	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071192	1.00[ASN][1000 genomes]
rs7071897	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7073651	0.95[ASN][1000 genomes]
rs7077692	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[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	1.00[ASN][1000 genomes]
rs7084525	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[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	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7088214	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7090293	0.90[ASN][1000 genomes]
rs7091578	1.00[ASN][1000 genomes]
rs7095070	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098313	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099975	1.00[ASN][1000 genomes]
rs7101352	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7895235	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895709	0.82[AMR][1000 genomes]
rs7907153	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10829140	NSUN6	cis	Skin Sun Exposed Lower leg	GTEx
rs10829140	RP11-499P20.2	cis	lung	GTEx
rs10829140	NSUN6	cis	Adipose Subcutaneous	GTEx
rs10829140	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs10829140	NSUN6	cis	Nerve Tibial	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18941000-18945800	Weak transcription	Left Ventricle	heart
2	chr10:18941000-18947200	Weak transcription	Pancreas	Pancrea
3	chr10:18941000-18947200	Weak transcription	Thymus	Thymus
4	chr10:18941000-18947400	Weak transcription	Gastric	stomach
5	chr10:18941200-18946600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr10:18941200-18946600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:18941200-18946800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr10:18941200-18946800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr10:18941200-18946800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr10:18941200-18946800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr10:18941200-18946800	Weak transcription	NH-A	brain
12	chr10:18941200-18946800	Weak transcription	NHLF	lung
13	chr10:18941200-18947000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:18941200-18947000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr10:18941200-18947000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr10:18941200-18947000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr10:18941200-18947000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr10:18941200-18947000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr10:18941200-18947000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr10:18941200-18947000	Weak transcription	Brain Anterior Caudate	brain
21	chr10:18941200-18947000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:18941200-18947000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr10:18941200-18947000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr10:18941200-18947000	Weak transcription	Brain Substantia Nigra	brain
25	chr10:18941200-18947000	Weak transcription	Fetal Brain Male	brain
26	chr10:18941200-18947000	Weak transcription	Fetal Stomach	stomach
27	chr10:18941200-18947000	Weak transcription	Psoas Muscle	Psoas
28	chr10:18941200-18947000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr10:18941200-18947000	Weak transcription	HMEC	breast
30	chr10:18941200-18947000	Weak transcription	NHEK	skin
31	chr10:18941200-18947200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr10:18941200-18947200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr10:18941200-18947200	Weak transcription	Fetal Thymus	thymus
34	chr10:18941200-18947200	Weak transcription	HUVEC	blood vessel
35	chr10:18941400-18946000	Weak transcription	HepG2	liver
36	chr10:18941400-18946800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr10:18941400-18946800	Weak transcription	Adipose Nuclei	Adipose
38	chr10:18941400-18946800	Weak transcription	Fetal Heart	heart
39	chr10:18941400-18946800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr10:18941400-18947000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr10:18941400-18947000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr10:18941400-18947000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:18941400-18947000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr10:18941400-18947000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr10:18941400-18947000	Weak transcription	Brain Angular Gyrus	brain
46	chr10:18941400-18947000	Weak transcription	Colon Smooth Muscle	Colon
47	chr10:18941400-18947000	Weak transcription	A549	lung
48	chr10:18941400-18947200	Weak transcription	Primary B cells from cord blood	blood
49	chr10:18941400-18947200	Weak transcription	Brain Hippocampus Middle	brain
50	chr10:18941400-18947400	Weak transcription	Brain Germinal Matrix	brain

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