Variant report

Variant	rs1776454
Chromosome Location	chr6:37482099-37482100
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:37479736..37486031-chr6:37501228..37507298,5	K562	blood:
2	chr6:37462097..37469080-chr6:37478016..37487473,13	K562	blood:
3	chr6:37465742..37467547-chr6:37480030..37482187,2	MCF-7	breast:
4	chr6:37475829..37477406-chr6:37481172..37483865,2	MCF-7	breast:
5	chr6:37470529..37472896-chr6:37481415..37484376,2	MCF-7	breast:
6	chr6:37481500..37483370-chr6:37521336..37524013,2	MCF-7	breast:
7	chr6:37479736..37482449-chr6:37501228..37503661,2	K562	blood:
8	chr6:37481015..37486178-chr6:37494019..37498263,5	MCF-7	breast:
9	chr6:37480410..37482550-chr6:37489261..37491673,2	K562	blood:
10	chr6:37481086..37482892-chr6:37484218..37487201,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263926	Chromatin interaction
ENSG00000198937	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10807184	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947675	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11969056	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12202055	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12202664	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211110	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1757186	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1757188	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757189	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757191	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1776455	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488540	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2776870	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776872	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2776874	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2776920	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2797795	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2797796	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2797798	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2797799	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818985	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818986	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3818987	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4714070	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4714071	0.82[AMR][1000 genomes]
rs62408395	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6903910	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6921922	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882322	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs914348	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9349039	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366935	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369005	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380677	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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
rs1776454	RP1-153P14.8	cis	Whole Blood	GTEx
rs1776454	RP1-153P14.5	cis	lung	GTEx
rs1776454	RP1-153P14.5	cis	Whole Blood	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37468000-37483600	Enhancers	Fetal Thymus	thymus
2	chr6:37471200-37483600	Weak transcription	Spleen	Spleen
3	chr6:37473800-37482200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:37476200-37483600	Enhancers	Thymus	Thymus
5	chr6:37476800-37482200	Weak transcription	GM12878-XiMat	blood
6	chr6:37478800-37482200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr6:37478800-37482400	Enhancers	Primary T cells from cord blood	blood
8	chr6:37478800-37482400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr6:37478800-37482400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:37479000-37482200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr6:37479000-37486400	Enhancers	Fetal Brain Female	brain
12	chr6:37479000-37486800	Enhancers	Fetal Brain Male	brain
13	chr6:37479200-37483800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr6:37479400-37482200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:37479400-37483200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:37479400-37483600	Weak transcription	Right Atrium	heart
17	chr6:37479400-37486200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:37479600-37482400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr6:37480000-37482600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:37480200-37482400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:37480400-37482600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:37480400-37483600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:37480600-37482200	Weak transcription	Esophagus	oesophagus
24	chr6:37480600-37484000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr6:37481000-37482400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:37481000-37482800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr6:37481200-37483000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:37481200-37483600	Enhancers	Brain Germinal Matrix	brain
29	chr6:37481200-37483800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:37481200-37484200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:37481200-37485600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:37481600-37482600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:37481600-37482800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
34	chr6:37481600-37483000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
35	chr6:37481600-37483200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:37481600-37484600	Enhancers	H9 Cell Line	embryonic stem cell
37	chr6:37481600-37485400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:37481600-37486200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:37481800-37482200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
40	chr6:37481800-37482400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
41	chr6:37481800-37483000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:37481800-37483000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
43	chr6:37481800-37483600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:37481800-37486200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr6:37482000-37482200	Enhancers	Brain Substantia Nigra	brain
46	chr6:37482000-37482200	Bivalent Enhancer	Osteobl	bone
47	chr6:37482000-37482400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:37482000-37482400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
49	chr6:37482000-37482400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:37482000-37482600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--

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