Variant report

Variant	rs28404075
Chromosome Location	chr8:19504289-19504290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10101438	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10282953	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10283283	1.00[ASN][1000 genomes]
rs17128770	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28483049	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2957618	0.85[ASN][1000 genomes]
rs4273864	0.92[ASN][1000 genomes]
rs4922074	0.92[ASN][1000 genomes]
rs6421414	0.92[ASN][1000 genomes]
rs7001715	0.92[ASN][1000 genomes]
rs7017890	0.85[ASN][1000 genomes]
rs73214673	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
2	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv890627	chr8:19389865-19561997	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv610754	chr8:19419494-19525294	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1025271	chr8:19435147-19574969	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1015448	chr8:19474715-19520367	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv6106	chr8:19499554-19544249	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28404075	ChGn	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19482000-19520000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr8:19495800-19508600	Weak transcription	Primary T cells from cord blood	blood
3	chr8:19498200-19508200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr8:19499600-19508200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr8:19500400-19504600	Weak transcription	NHDF-Ad	bronchial
6	chr8:19500400-19510600	Weak transcription	NHLF	lung
7	chr8:19500400-19519600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:19501000-19510800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr8:19501400-19504400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr8:19502200-19506200	Enhancers	Brain Substantia Nigra	brain
11	chr8:19502400-19504400	Enhancers	Brain Anterior Caudate	brain
12	chr8:19502600-19505600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr8:19503000-19505400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr8:19503000-19508000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr8:19503000-19513600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr8:19503200-19504600	Weak transcription	Lung	lung
17	chr8:19503200-19504800	Weak transcription	Fetal Lung	lung
18	chr8:19503200-19507000	Enhancers	A549	lung
19	chr8:19503200-19508200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr8:19503200-19510800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr8:19503200-19511000	Weak transcription	Hela-S3	cervix
22	chr8:19503400-19504400	Weak transcription	Brain Angular Gyrus	brain
23	chr8:19503400-19504400	Weak transcription	Esophagus	oesophagus
24	chr8:19503400-19504400	Weak transcription	Left Ventricle	heart
25	chr8:19503400-19504400	Weak transcription	Ovary	ovary
26	chr8:19503400-19504400	Weak transcription	Right Atrium	heart
27	chr8:19503400-19504800	Enhancers	Fetal Heart	heart
28	chr8:19503400-19505400	Weak transcription	Spleen	Spleen
29	chr8:19503400-19510800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr8:19503400-19510800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr8:19503400-19518200	Weak transcription	Primary B cells from cord blood	blood
32	chr8:19503400-19521000	Weak transcription	Pancreas	Pancrea
33	chr8:19503600-19505400	Weak transcription	Brain Hippocampus Middle	brain
34	chr8:19504000-19506200	Enhancers	Brain Cingulate Gyrus	brain
35	chr8:19504000-19506400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr8:19504200-19504800	Enhancers	Brain Germinal Matrix	brain
37	chr8:19504200-19504800	Enhancers	Right Ventricle	heart
38	chr8:19504200-19505000	Enhancers	Primary B cells from peripheral blood	blood
39	chr8:19504200-19506000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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