Variant report

Variant	rs11969056
Chromosome Location	chr6:37484285-37484286
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:37479736..37486031-chr6:37501228..37507298,5	K562	blood:
2	chr6:37477707..37479508-chr6:37482830..37484722,3	K562	blood:
3	chr6:37462097..37469080-chr6:37478016..37487473,13	K562	blood:
4	chr6:37481086..37482892-chr6:37484218..37487201,2	K562	blood:
5	chr6:37483817..37486098-chr6:37619708..37622171,2	MCF-7	breast:
6	chr6:37470529..37472896-chr6:37481415..37484376,2	MCF-7	breast:
7	chr6:37460921..37462916-chr6:37482767..37484311,2	MCF-7	breast:
8	chr6:37448210..37451010-chr6:37482118..37484936,2	K562	blood:
9	chr6:37481015..37486178-chr6:37494019..37498263,5	MCF-7	breast:
10	chr6:37483726..37486812-chr6:37495696..37499508,4	K562	blood:
11	chr1:115052767..115054664-chr6:37483725..37485853,2	MCF-7	breast:
12	chr6:37482557..37484307-chr6:37512336..37515157,3	MCF-7	breast:
13	chr6:37483822..37487083-chr6:37490649..37493526,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197323	Chromatin interaction
ENSG00000227920	Chromatin interaction
ENSG00000198937	Chromatin interaction
ENSG00000229559	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10807184	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10947675	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12202055	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12202664	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757186	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757188	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757189	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757191	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1776454	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1776455	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2488540	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2776870	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2776872	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2776874	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2776920	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2797795	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2797796	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2797798	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2797799	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3818985	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818986	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3818987	0.87[AMR][1000 genomes];0.83[EUR][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	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs882322	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs914348	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9349039	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366935	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9369005	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380677	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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
rs11969056	RP1-153P14.8	cis	Whole Blood	GTEx
rs11969056	RP1-153P14.5	cis	Whole Blood	GTEx
rs11969056	RP1-153P14.5	cis	lung	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

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	chr6:37481600-37484600	Enhancers	H9 Cell Line	embryonic stem cell
6	chr6:37481600-37485400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:37481600-37486200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:37481800-37486200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr6:37482000-37484400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:37482000-37485000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:37482000-37485000	Enhancers	NHEK	skin
12	chr6:37482000-37485400	Enhancers	HMEC	breast
13	chr6:37482000-37485600	Enhancers	Primary B cells from peripheral blood	blood
14	chr6:37482200-37485400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr6:37482200-37485400	Enhancers	Esophagus	oesophagus
16	chr6:37482200-37485800	Enhancers	Brain Cingulate Gyrus	brain
17	chr6:37482400-37484600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:37482400-37485600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:37482400-37485600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:37482400-37486200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr6:37482400-37486400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr6:37482600-37484400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
23	chr6:37482600-37485400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr6:37482600-37485600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:37482800-37484600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:37482800-37484600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:37482800-37485200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr6:37483000-37484400	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr6:37483000-37484600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:37483000-37485400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr6:37483000-37485800	Enhancers	Fetal Intestine Small	intestine
32	chr6:37483200-37484600	Enhancers	Placenta	Placenta
33	chr6:37483200-37485200	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr6:37483400-37484400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr6:37483400-37484400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:37483400-37484400	Enhancers	Stomach Smooth Muscle	stomach
37	chr6:37483400-37484600	Bivalent Enhancer	Stomach Mucosa	stomach
38	chr6:37483400-37484800	Enhancers	Brain Angular Gyrus	brain
39	chr6:37483400-37485000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:37483400-37485000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:37483400-37485000	Enhancers	Fetal Intestine Large	intestine
42	chr6:37483400-37485200	Enhancers	Primary B cells from cord blood	blood
43	chr6:37483400-37485200	Flanking Active TSS	Dnd41	blood
44	chr6:37483400-37485400	Enhancers	Adipose Nuclei	Adipose
45	chr6:37483400-37485600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:37483400-37486400	Enhancers	Primary hematopoietic stem cells	blood
47	chr6:37483400-37486400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:37483400-37486400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr6:37483600-37484400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:37483600-37484400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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