Variant report

Variant	rs10828967
Chromosome Location	chr10:18882432-18882433
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	chr10:18881247..18884169-chr10:18946476..18949026,2	K562	blood:
2	chr10:18881247..18884193-chr10:18945949..18949026,3	K562	blood:

Variant related genes	Relation type
ENSG00000165997	Chromatin interaction
ENSG00000152487	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10430567	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10734063	0.81[AMR][1000 genomes]
rs10741115	0.81[AMR][1000 genomes]
rs10764583	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10764600	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10764601	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10764602	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10764603	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10764604	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10764605	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10764625	0.81[ASN][1000 genomes]
rs10828896	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10828911	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10828965	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10828975	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10828983	0.83[ASN][1000 genomes]
rs10828984	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10828991	0.81[ASN][1000 genomes]
rs10829009	0.81[ASN][1000 genomes]
rs10829037	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10829039	0.81[AMR][1000 genomes]
rs11014892	0.82[AMR][1000 genomes]
rs11015048	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11015077	0.83[ASN][1000 genomes]
rs11015196	0.81[AMR][1000 genomes]
rs11525266	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12569474	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3817494	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4748488	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4748492	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs5022622	0.81[ASN][1000 genomes]
rs56410858	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57579336	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62634837	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62634838	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62636218	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6482533	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7077722	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7079325	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7100880	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72787951	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72787963	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7477076	0.81[ASN][1000 genomes]
rs7894016	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7895784	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7901598	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7904263	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv34545	chr10:18821185-18908294	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv1793653	chr10:18827828-18888369	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1794817	chr10:18827828-18888369	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv1811259	chr10:18827828-18888369	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	esv1840241	chr10:18827828-18888369	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv1841068	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	esv1851495	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	esv2757371	chr10:18835325-18906507	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv2759736	chr10:18835325-18906507	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv466760	chr10:18839350-18905935	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv550044	chr10:18839350-18905935	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10828967	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs10828967	NSUN6	cis	lung	GTEx
rs10828967	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs10828967	RP11-499P20.2	cis	Whole Blood	GTEx
rs10828967	RP11-499P20.2	cis	lung	GTEx
rs10828967	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs10828967	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs10828967	RP11-499P20.2	cis	Thyroid	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18842000-18886400	Weak transcription	Colon Smooth Muscle	Colon
2	chr10:18846200-18899200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:18848400-18915800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr10:18849800-18910800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr10:18861000-18883200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr10:18862200-18894600	Weak transcription	HSMM	muscle
7	chr10:18863000-18894600	Weak transcription	A549	lung
8	chr10:18863000-18910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:18863800-18902200	Weak transcription	Brain Anterior Caudate	brain
10	chr10:18864800-18898000	Weak transcription	Fetal Kidney	kidney
11	chr10:18865600-18885000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr10:18866600-18899400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr10:18867600-18894400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr10:18867600-18899600	Weak transcription	Placenta	Placenta
15	chr10:18867800-18900400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr10:18867800-18916400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr10:18868000-18896400	Weak transcription	NHEK	skin
18	chr10:18868000-18902200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr10:18868000-18916200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr10:18868200-18896600	Weak transcription	Small Intestine	intestine
21	chr10:18868200-18904800	Weak transcription	HSMMtube	muscle
22	chr10:18868800-18896600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr10:18869800-18910800	Weak transcription	Right Ventricle	heart
24	chr10:18870000-18884000	Weak transcription	Aorta	Aorta
25	chr10:18870200-18892000	Weak transcription	HepG2	liver
26	chr10:18870200-18900600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr10:18870400-18884000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr10:18870400-18884000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr10:18870400-18894400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr10:18870600-18884000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr10:18870600-18884000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr10:18870600-18908400	Weak transcription	Brain Substantia Nigra	brain
33	chr10:18870600-18916000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr10:18871000-18896400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr10:18871400-18895000	Weak transcription	Fetal Brain Male	brain
36	chr10:18871600-18910000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr10:18872000-18887200	Weak transcription	Fetal Heart	heart
38	chr10:18872400-18883600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr10:18872400-18885400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:18872400-18895000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr10:18872400-18899600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr10:18872800-18916000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:18873000-18894600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr10:18873200-18908200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr10:18873400-18883600	Weak transcription	Fetal Lung	lung
46	chr10:18873600-18896800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr10:18873600-18916000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr10:18875000-18916000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr10:18875400-18884000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr10:18875600-18894600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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