Variant report

Variant	rs12679834
Chromosome Location	chr8:19820433-19820434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:19796366..19798853-chr8:19819344..19821479,2	K562	blood:
2	chr8:19811879..19814750-chr8:19820326..19823164,2	K562	blood:
3	chr8:19820325..19822189-chr8:19825271..19827083,2	K562	blood:

Variant related genes	Relation type
ENSG00000175445	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10096633	0.93[ASN][1000 genomes]
rs1011685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1059611	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11570891	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11989309	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11991231	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12678603	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12678604	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12678919	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1569209	0.81[EUR][1000 genomes]
rs17091909	0.95[ASN][1000 genomes]
rs17411024	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17411113	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17482753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1803924	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28675909	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735964	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6586884	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6983430	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6999813	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7004149	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7004158	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7007609	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7007797	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7016880	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7819706	0.93[ASN][1000 genomes]
rs7841189	0.95[ASN][1000 genomes]
rs9644568	0.83[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][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	nsv610759	chr8:19561997-20068842	Enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498082	chr8:19722435-19873112	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv32767	chr8:19740189-19873082	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv1033511	chr8:19751299-20625091	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv890632	chr8:19816371-19853146	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12679834	LPL	cis	multi-tissue	Pritchard

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19798600-19824200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr8:19800800-19823000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:19805000-19824800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr8:19805800-19824600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:19811800-19822400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr8:19811800-19826000	Weak transcription	Brain Germinal Matrix	brain
7	chr8:19813600-19823000	Weak transcription	Fetal Brain Male	brain
8	chr8:19814200-19821600	Weak transcription	Fetal Brain Female	brain
9	chr8:19814800-19822800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr8:19817000-19824800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr8:19818400-19822800	Strong transcription	Fetal Lung	lung
12	chr8:19819000-19820600	Genic enhancers	Fetal Heart	heart
13	chr8:19819200-19820600	Genic enhancers	Adipose Nuclei	Adipose
14	chr8:19819200-19820800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr8:19819200-19821000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr8:19819400-19820600	Enhancers	Primary B cells from peripheral blood	blood
17	chr8:19819400-19820600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr8:19819400-19820600	Strong transcription	Ovary	ovary
19	chr8:19819400-19820800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr8:19819600-19820600	Enhancers	Primary B cells from cord blood	blood
21	chr8:19819600-19820600	Enhancers	Primary hematopoietic stem cells	blood
22	chr8:19819600-19820600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr8:19819600-19822200	Strong transcription	Right Ventricle	heart
24	chr8:19819800-19820600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr8:19819800-19820600	Enhancers	Placenta	Placenta
26	chr8:19820000-19820600	Enhancers	Psoas Muscle	Psoas
27	chr8:19820000-19822000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr8:19820000-19822200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr8:19820000-19822600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr8:19820000-19823600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr8:19820200-19820600	Strong transcription	Lung	lung
32	chr8:19820200-19821000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr8:19820200-19822000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr8:19820200-19824000	Strong transcription	Left Ventricle	heart
35	chr8:19820400-19820600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr8:19820400-19820600	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr8:19820400-19821600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr8:19820400-19821800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr8:19820400-19822000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr8:19820400-19822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr8:19820400-19825400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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