Variant report

Variant	rs1589079
Chromosome Location	chr8:52836299-52836300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10087958	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10504130	0.82[JPT][hapmap]
rs10958305	0.83[JPT][hapmap]
rs11775587	0.82[JPT][hapmap]
rs11775611	0.82[JPT][hapmap]
rs11781330	0.85[JPT][hapmap]
rs11785805	0.82[JPT][hapmap]
rs12541693	0.88[JPT][hapmap]
rs12544872	0.81[JPT][hapmap]
rs12546159	0.88[JPT][hapmap]
rs16916856	0.82[JPT][hapmap]
rs16916865	0.82[JPT][hapmap]
rs16916966	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16916968	0.94[CHB][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17284746	0.82[JPT][hapmap]
rs2138297	0.93[ASN][1000 genomes]
rs2176119	0.93[ASN][1000 genomes]
rs41453644	0.82[JPT][hapmap]
rs6473666	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473667	0.86[EUR][1000 genomes]
rs6768	0.81[JPT][hapmap]
rs6994203	0.83[JPT][hapmap]
rs7813414	0.89[ASN][1000 genomes]
rs7814421	0.84[EUR][1000 genomes]
rs7819892	0.91[ASN][1000 genomes]
rs7820177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7833668	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7834181	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs877248	0.94[CHB][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
4	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1589079	LOC286071	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52813400-52837200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr8:52813600-52837400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr8:52813800-52837400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr8:52814000-52837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr8:52814000-52839200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:52814200-52842000	Weak transcription	Brain Substantia Nigra	brain
7	chr8:52814200-52850000	Weak transcription	Spleen	Spleen
8	chr8:52814800-52837200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr8:52815000-52852000	Weak transcription	Colon Smooth Muscle	Colon
10	chr8:52815200-52837400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr8:52822400-52837800	Weak transcription	Esophagus	oesophagus
12	chr8:52822600-52860200	Weak transcription	Fetal Muscle Leg	muscle
13	chr8:52823000-52840200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr8:52823600-52838200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr8:52827600-52836600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr8:52831200-52838800	Weak transcription	Left Ventricle	heart
17	chr8:52831200-52840800	Weak transcription	Right Ventricle	heart
18	chr8:52831600-52837200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr8:52831800-52841000	Weak transcription	Lung	lung
20	chr8:52831800-52858400	Weak transcription	Primary T cells from cord blood	blood
21	chr8:52831800-52863400	Weak transcription	Aorta	Aorta
22	chr8:52832000-52836400	Weak transcription	Fetal Stomach	stomach
23	chr8:52832000-52838400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr8:52835200-52837600	Weak transcription	Pancreas	Pancrea
25	chr8:52835400-52837200	Weak transcription	Primary B cells from cord blood	blood
26	chr8:52835400-52837800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr8:52835400-52840200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr8:52835600-52837400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr8:52835600-52837400	Weak transcription	Psoas Muscle	Psoas
30	chr8:52835800-52836400	Strong transcription	Ovary	ovary
31	chr8:52835800-52836800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr8:52835800-52837000	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr8:52835800-52837800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr8:52836000-52837200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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