Variant report

Variant	rs2409729
Chromosome Location	chr8:11051256-11051257
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10087767	1.00[CHB][hapmap]
rs10088853	1.00[CHB][hapmap]
rs10095003	1.00[ASN][1000 genomes]
rs10100660	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10101329	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10110684	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10503417	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10903337	1.00[CHB][hapmap]
rs11775489	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11776603	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11777355	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777887	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777918	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778121	1.00[CHB][hapmap]
rs11783045	1.00[CHB][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11783890	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11785237	1.00[ASN][1000 genomes]
rs11785392	1.00[CHB][hapmap]
rs11989369	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13248014	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13248264	1.00[CHB][hapmap]
rs13248300	1.00[CHB][hapmap]
rs13249916	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13251528	1.00[CHB][hapmap]
rs13256743	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13265553	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13266785	1.00[ASN][1000 genomes]
rs13273857	1.00[CHB][hapmap]
rs13276708	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13276836	1.00[CHB][hapmap]
rs17152841	1.00[CHB][hapmap]
rs17725480	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17725534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17726209	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17779791	1.00[CHB][hapmap]
rs17782536	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17782554	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1987190	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409691	1.00[CHB][hapmap]
rs2409692	1.00[CHB][hapmap]
rs2409693	1.00[CHB][hapmap]
rs2409695	1.00[CHB][hapmap]
rs2409719	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2409720	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409725	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409726	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409730	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3021495	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3021497	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3021498	1.00[ASN][1000 genomes]
rs3021501	1.00[ASN][1000 genomes]
rs34309263	1.00[ASN][1000 genomes]
rs34367737	1.00[ASN][1000 genomes]
rs35211404	1.00[ASN][1000 genomes]
rs4291231	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4412337	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4451268	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618656	1.00[CHB][hapmap]
rs4642600	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4840548	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4841486	1.00[CHB][hapmap]
rs4841497	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4841499	1.00[ASN][1000 genomes]
rs6601561	1.00[CHB][hapmap]
rs6601563	1.00[CHB][hapmap]
rs67418928	1.00[ASN][1000 genomes]
rs67559300	1.00[ASN][1000 genomes]
rs71518512	1.00[ASN][1000 genomes]
rs73198943	1.00[ASN][1000 genomes]
rs7832722	1.00[CHB][hapmap]
rs7844536	0.80[AMR][1000 genomes]
rs9329238	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657544	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2409729	C8orf5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11028200-11052400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr8:11028200-11056600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr8:11028800-11054400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr8:11029600-11056800	Weak transcription	Fetal Intestine Small	intestine
5	chr8:11031400-11054200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr8:11032000-11053800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr8:11034600-11054400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr8:11034600-11057000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:11034600-11057000	Weak transcription	Esophagus	oesophagus
10	chr8:11035400-11054600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr8:11035600-11054000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:11035800-11051600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr8:11035800-11056000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr8:11039400-11052200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr8:11040600-11054200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr8:11041000-11051600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr8:11041600-11054200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:11042200-11055000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr8:11042800-11056600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr8:11044800-11054800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr8:11045200-11053600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr8:11045200-11057000	Weak transcription	Fetal Stomach	stomach
23	chr8:11045400-11054000	Weak transcription	Fetal Brain Female	brain
24	chr8:11045600-11056000	Weak transcription	NHEK	skin
25	chr8:11046000-11054200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr8:11046000-11054200	Weak transcription	HMEC	breast
27	chr8:11046200-11054000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr8:11046400-11054200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr8:11046400-11056600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr8:11046600-11054000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr8:11046600-11054200	Weak transcription	HSMM	muscle
32	chr8:11046600-11054400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr8:11046600-11056600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr8:11046800-11053800	Weak transcription	HSMMtube	muscle
35	chr8:11048600-11052200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr8:11048600-11054800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr8:11049000-11056800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr8:11049200-11051600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr8:11050000-11054200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr8:11050400-11057000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr8:11050600-11051800	Weak transcription	GM12878-XiMat	blood
42	chr8:11050600-11053800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr8:11050600-11054400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr8:11050600-11054600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr8:11050600-11056400	Weak transcription	Small Intestine	intestine
46	chr8:11050800-11053600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr8:11051000-11052200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr8:11051000-11054800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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