Variant report

Variant	rs680009
Chromosome Location	chr6:24950829-24950830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1328714	0.83[EUR][1000 genomes]
rs369964	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs391867	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs435086	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9467356	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][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	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv275111	chr6:24946671-24951199	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs680009	PRL	cis	parietal	SCAN
rs680009	HIST1H3F	cis	cerebellum	SCAN
rs680009	GPLD1	cis	cerebellum	SCAN
rs680009	GPX6	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24946400-24951600	Enhancers	Primary B cells from peripheral blood	blood
2	chr6:24947800-24953600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:24948400-24954600	Enhancers	Fetal Thymus	thymus
4	chr6:24948400-24955800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:24949000-24951000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
6	chr6:24949000-24951000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:24949000-24951000	Weak transcription	Spleen	Spleen
8	chr6:24949200-24951200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:24949200-24951200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:24949200-24952800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr6:24949200-24952800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr6:24949200-24953400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr6:24949400-24951400	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:24949400-24951800	Enhancers	Thymus	Thymus
15	chr6:24949400-24953200	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr6:24949600-24952800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:24949600-24952800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr6:24949800-24951400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:24949800-24952000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:24949800-24952400	Weak transcription	Colonic Mucosa	Colon
21	chr6:24949800-24952800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr6:24950000-24951600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr6:24950000-24951600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:24950200-24952000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr6:24950200-24952200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:24950200-24952400	Enhancers	Fetal Lung	lung
27	chr6:24950400-24952000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:24950400-24988600	Weak transcription	Dnd41	blood
29	chr6:24950600-24953200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:24950800-24951000	Flanking Active TSS	GM12878-XiMat	blood
31	chr6:24950800-24951200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:24950800-24951200	Enhancers	Primary B cells from cord blood	blood
33	chr6:24950800-24951200	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr6:24950800-24951600	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr6:24950800-24951600	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr6:24950800-24952800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr6:24950800-24952800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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