Variant report

Variant	rs28507159
Chromosome Location	chr8:11166076-11166077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10098322	0.83[AFR][1000 genomes]
rs10099569	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10104728	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10107010	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11250127	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11774673	0.81[AFR][1000 genomes]
rs11775635	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11782706	0.87[AFR][1000 genomes]
rs11784458	0.84[AFR][1000 genomes]
rs11784544	0.82[AFR][1000 genomes]
rs11994376	0.81[AFR][1000 genomes]
rs13270679	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13279067	0.83[EUR][1000 genomes]
rs17797443	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1897950	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1897951	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2060465	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2099456	0.81[EUR][1000 genomes]
rs2164272	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2164273	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2293855	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293856	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2572419	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3174048	0.90[AFR][1000 genomes]
rs35392635	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35631424	0.80[AFR][1000 genomes]
rs3779891	0.90[AFR][1000 genomes]
rs3808509	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3808513	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3808518	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3808519	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4559208	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4568582	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4840554	0.82[EUR][1000 genomes]
rs58283816	0.81[AFR][1000 genomes]
rs6601578	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6601579	0.83[EUR][1000 genomes]
rs6601580	0.84[AFR][1000 genomes]
rs6984759	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6985146	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6985460	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6988922	0.83[AFR][1000 genomes]
rs6991074	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6991606	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7003241	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7004362	0.85[EUR][1000 genomes]
rs7005469	0.83[AFR][1000 genomes]
rs7016671	0.90[AFR][1000 genomes]
rs718427	0.83[EUR][1000 genomes]
rs7815804	0.87[AFR][1000 genomes]
rs7816601	0.82[AFR][1000 genomes]
rs7816636	0.82[AFR][1000 genomes]
rs7831346	0.84[AFR][1000 genomes]
rs7833966	0.82[AFR][1000 genomes]
rs7837036	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7838897	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1033312	chr8:11126800-11252170	Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28507159	THEX1	Cis_chr	lymphoblastoid	RTeQTL
rs28507159	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs28507159	MTMR9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11143000-11166400	Weak transcription	Esophagus	oesophagus
2	chr8:11143000-11166400	Weak transcription	Pancreas	Pancrea
3	chr8:11143400-11166400	Weak transcription	HSMMtube	muscle
4	chr8:11143800-11169000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr8:11146800-11166200	Weak transcription	Spleen	Spleen
6	chr8:11147600-11166400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr8:11150800-11169800	Weak transcription	Small Intestine	intestine
8	chr8:11152000-11168200	Weak transcription	Fetal Heart	heart
9	chr8:11152000-11169800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr8:11154000-11166600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr8:11154000-11167000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr8:11154200-11166400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr8:11154200-11166400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr8:11154200-11181400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr8:11154200-11183800	Strong transcription	Liver	Liver
16	chr8:11154600-11183000	Strong transcription	Fetal Muscle Trunk	muscle
17	chr8:11155000-11184000	Strong transcription	Dnd41	blood
18	chr8:11155600-11183200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr8:11157200-11180800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr8:11157400-11182600	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr8:11157600-11183000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr8:11157800-11166200	Weak transcription	HMEC	breast
23	chr8:11160000-11176200	Strong transcription	Fetal Thymus	thymus
24	chr8:11160600-11169800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr8:11160600-11176200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr8:11160600-11176200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr8:11160600-11178800	Strong transcription	Fetal Intestine Large	intestine
28	chr8:11161000-11169600	Strong transcription	Fetal Stomach	stomach
29	chr8:11161600-11183200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr8:11161800-11182600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr8:11162000-11170200	Strong transcription	Rectal Smooth Muscle	rectum
32	chr8:11162000-11180200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr8:11162000-11181200	Strong transcription	HSMM	muscle
34	chr8:11162000-11182600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr8:11162000-11183400	Strong transcription	Primary T cells from cord blood	blood
36	chr8:11162200-11168000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr8:11162200-11169400	Strong transcription	Primary hematopoietic stem cells	blood
38	chr8:11162200-11176200	Strong transcription	Primary B cells from cord blood	blood
39	chr8:11162200-11180600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr8:11162200-11181000	Strong transcription	Placenta	Placenta
41	chr8:11162200-11181600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr8:11162200-11183200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr8:11162400-11166800	Strong transcription	NHEK	skin
44	chr8:11162400-11169000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr8:11162400-11169200	Strong transcription	Hela-S3	cervix
46	chr8:11162400-11169400	Strong transcription	NHDF-Ad	bronchial
47	chr8:11162400-11171000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr8:11162400-11171200	Strong transcription	Fetal Lung	lung
49	chr8:11162400-11172800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr8:11162400-11173800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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