Variant report

Variant	rs10829213
Chromosome Location	chr10:18973339-18973340
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18962456..18966517-chr10:18966877..18973376,6	K562	blood:
2	chr10:18969086..18970965-chr10:18973281..18975325,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1027193	0.82[ASN][1000 genomes]
rs1055116	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10734063	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10741111	0.83[ASN][1000 genomes]
rs10741115	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10741129	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10741132	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10764582	0.82[AMR][1000 genomes]
rs10764600	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10764601	0.85[AMR][1000 genomes]
rs10764603	0.85[AMR][1000 genomes]
rs10764625	0.81[ASN][1000 genomes]
rs10764640	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10764691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828870	0.82[AMR][1000 genomes]
rs10828871	0.82[AMR][1000 genomes]
rs10828872	0.86[AMR][1000 genomes]
rs10828896	0.84[AMR][1000 genomes]
rs10828911	0.87[AMR][1000 genomes]
rs10828965	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10828975	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10828991	0.81[ASN][1000 genomes]
rs10829009	0.81[ASN][1000 genomes]
rs10829022	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10829037	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10829039	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10829040	0.83[AMR][1000 genomes]
rs10829058	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10829060	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10829070	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10829148	0.89[EUR][1000 genomes]
rs10829151	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11014892	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11015048	0.87[AMR][1000 genomes]
rs11015196	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11015255	0.87[AMR][1000 genomes]
rs11015312	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11015421	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11525266	0.84[AMR][1000 genomes]
rs11540309	0.92[ASN][1000 genomes]
rs12219183	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12359758	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12569474	0.84[AMR][1000 genomes]
rs12782882	0.82[ASN][1000 genomes]
rs2272274	0.82[AMR][1000 genomes]
rs3740102	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4747350	0.81[AMR][1000 genomes]
rs4748488	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4748492	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4748509	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5022622	0.81[ASN][1000 genomes]
rs57066269	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57579336	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62636218	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6482533	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6482597	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7077722	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7079325	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7081461	0.81[ASN][1000 genomes]
rs7081690	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7081977	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7087030	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7099260	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7100880	0.85[ASN][1000 genomes]
rs72787963	0.85[AMR][1000 genomes]
rs7894016	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7896918	0.88[ASN][1000 genomes]
rs7898781	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7899017	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7901598	0.87[AMR][1000 genomes]
rs7904263	0.85[AMR][1000 genomes]
rs7909570	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909845	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7910902	0.97[ASN][1000 genomes]
rs7917584	0.83[AMR][1000 genomes]
rs7922005	0.90[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10829213	ARL5B	cis	multi-tissue	Pritchard
rs10829213	NSUN6	cis	lung	GTEx
rs10829213	RP11-499P20.2	cis	Thyroid	GTEx
rs10829213	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs10829213	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs10829213	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs10829213	RP11-499P20.2	cis	Whole Blood	GTEx
rs10829213	RP11-499P20.2	cis	lung	GTEx
rs10829213	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs10829213	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs10829213	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18951000-18976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:18951400-18973800	Weak transcription	Aorta	Aorta
3	chr10:18954400-18973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:18959000-18973600	Weak transcription	Left Ventricle	heart
5	chr10:18960800-18973400	Weak transcription	Ovary	ovary
6	chr10:18961000-18973600	Weak transcription	Thymus	Thymus
7	chr10:18962400-18973600	Weak transcription	Fetal Intestine Small	intestine
8	chr10:18962400-18973600	Weak transcription	Fetal Stomach	stomach
9	chr10:18963200-18973400	Weak transcription	Pancreas	Pancrea
10	chr10:18964200-18973400	Weak transcription	Psoas Muscle	Psoas
11	chr10:18964600-18973600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr10:18964600-18973800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:18964800-18973400	Weak transcription	Fetal Brain Female	brain
14	chr10:18964800-18973400	Weak transcription	HUVEC	blood vessel
15	chr10:18964800-18973800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr10:18965000-18973400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr10:18965200-18973400	Weak transcription	Brain Germinal Matrix	brain
18	chr10:18965200-18973400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:18966200-18973400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:18966200-18973400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr10:18966200-18976000	Weak transcription	HepG2	liver
22	chr10:18966600-18973400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr10:18966600-18973400	Weak transcription	Primary B cells from cord blood	blood
24	chr10:18966600-18973400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:18966600-18973400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr10:18966600-18974600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr10:18966800-18973400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:18967200-18973400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr10:18968400-18978800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr10:18969800-18974200	Enhancers	Osteobl	bone
31	chr10:18969800-18974800	Enhancers	Hela-S3	cervix
32	chr10:18970000-18974200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr10:18970800-18973600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr10:18971000-18973600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr10:18971800-18973400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr10:18971800-18973400	Weak transcription	Fetal Lung	lung
37	chr10:18971800-18975000	Weak transcription	Dnd41	blood
38	chr10:18972200-18973600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:18972200-18974000	Weak transcription	Liver	Liver
40	chr10:18972600-18973400	Enhancers	NHEK	skin
41	chr10:18972600-18973600	Enhancers	A549	lung
42	chr10:18972600-18974200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr10:18972600-18974200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:18972800-18973400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr10:18973000-18973400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr10:18973000-18974000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr10:18973000-18974000	Weak transcription	HMEC	breast
48	chr10:18973200-18974400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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