Variant report

Variant	rs1776460
Chromosome Location	chr6:37485484-37485485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:37470263..37472144-chr6:37484814..37487547,2	K562	blood:
2	chr6:37479736..37486031-chr6:37501228..37507298,5	K562	blood:
3	chr6:37485310..37486812-chr6:37496622..37499508,2	K562	blood:
4	chr6:37484939..37487595-chr6:37488924..37490992,2	MCF-7	breast:
5	chr6:37462097..37469080-chr6:37478016..37487473,13	K562	blood:
6	chr6:37481086..37482892-chr6:37484218..37487201,2	K562	blood:
7	chr6:37483817..37486098-chr6:37619708..37622171,2	MCF-7	breast:
8	chr6:37481015..37486178-chr6:37494019..37498263,5	MCF-7	breast:
9	chr6:37483726..37486812-chr6:37495696..37499508,4	K562	blood:
10	chr1:115052767..115054664-chr6:37483725..37485853,2	MCF-7	breast:
11	chr6:37483822..37487083-chr6:37490649..37493526,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198937	Chromatin interaction
ENSG00000197323	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12202055	0.83[ASN][1000 genomes]
rs1757169	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1757171	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1757173	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1757174	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1757177	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757178	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757180	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1757181	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757183	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1776456	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2776875	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2776877	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2776878	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2797801	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2797803	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3818987	0.80[ASN][1000 genomes]
rs4711498	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4714072	0.81[AMR][1000 genomes]
rs62408395	0.82[ASN][1000 genomes]
rs914347	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914348	0.83[ASN][1000 genomes]
rs914349	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1016310	chr6:37473075-37528469	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1776460	RP1-153P14.5	cis	Whole Blood	GTEx
rs1776460	RP1-153P14.5	cis	lung	GTEx
rs1776460	RP1-153P14.8	cis	Whole Blood	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37479000-37486400	Enhancers	Fetal Brain Female	brain
2	chr6:37479000-37486800	Enhancers	Fetal Brain Male	brain
3	chr6:37479400-37486200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:37481200-37485600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:37481600-37486200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:37481800-37486200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr6:37482000-37485600	Enhancers	Primary B cells from peripheral blood	blood
8	chr6:37482200-37485800	Enhancers	Brain Cingulate Gyrus	brain
9	chr6:37482400-37485600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:37482400-37485600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:37482400-37486200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr6:37482400-37486400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr6:37482600-37485600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:37483000-37485800	Enhancers	Fetal Intestine Small	intestine
15	chr6:37483400-37485600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:37483400-37486400	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:37483400-37486400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:37483400-37486400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr6:37483600-37485600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:37483600-37486000	Flanking Active TSS	Thymus	Thymus
21	chr6:37483600-37486000	Flanking Active TSS	GM12878-XiMat	blood
22	chr6:37483600-37486200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr6:37483600-37486600	Flanking Active TSS	Fetal Thymus	thymus
24	chr6:37483800-37485800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
25	chr6:37483800-37486000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr6:37484000-37485600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:37484400-37486200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:37484400-37486400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:37484400-37486600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:37484400-37486800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr6:37484600-37485600	Enhancers	Brain Hippocampus Middle	brain
32	chr6:37484600-37485800	Weak transcription	Spleen	Spleen
33	chr6:37484600-37486200	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr6:37484600-37486200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:37484600-37486200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr6:37484600-37486200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:37484600-37486400	Enhancers	Brain Germinal Matrix	brain
38	chr6:37484600-37486600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:37484600-37487000	Weak transcription	Right Atrium	heart
40	chr6:37485000-37485600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:37485000-37486200	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr6:37485200-37485600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:37485200-37485600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:37485200-37485600	Enhancers	Brain Angular Gyrus	brain
45	chr6:37485200-37486000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:37485200-37486400	Enhancers	Duodenum Mucosa	Duodenum
47	chr6:37485200-37486400	Enhancers	Dnd41	blood
48	chr6:37485200-37486800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:37485200-37487400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:37485400-37485600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood

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