Variant report

Variant	rs6777340
Chromosome Location	chr3:52188308-52188309
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52015341..52017883-chr3:52186866..52188474,2	MCF-7	breast:
2	chr3:52186953..52189415-chr3:52231734..52233530,2	K562	blood:
3	chr3:52089814..52091351-chr3:52187528..52189873,2	K562	blood:
4	chr1:144533735..144534707-chr3:52187701..52188643,2	Hela-S3	cervix:
5	chr3:52025976..52031164-chr3:52185902..52190126,6	K562	blood:
6	chr3:52186178..52189000-chr3:52232033..52234935,2	K562	blood:
7	chr3:52031889..52035644-chr3:52185003..52188385,3	K562	blood:
8	chr3:52187270..52191492-chr3:52311211..52313437,5	MCF-7	breast:
9	chr3:52008016..52010191-chr3:52187253..52189980,2	MCF-7	breast:
10	chr3:52088633..52090447-chr3:52187469..52189147,2	MCF-7	breast:
11	chr3:52007628..52011282-chr3:52186808..52190381,5	K562	blood:
12	chr3:52187595..52189186-chr3:52321663..52323180,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272762	Chromatin interaction
ENSG00000023330	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000164086	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000248487	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000114786	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12386365	0.83[AFR][1000 genomes]
rs12495536	0.84[EUR][1000 genomes]
rs12496447	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12629791	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2334961	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28387060	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28452586	0.80[AFR][1000 genomes]
rs2878438	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs352152	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687607	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4687805	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687810	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773704	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6778442	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6786592	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs731684	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs735768	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747343	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs749995	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616695	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7644325	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs893055	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9828327	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9851576	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9874939	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52187200-52188400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:52187200-52188400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:52187200-52188400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:52187200-52188400	Flanking Active TSS	HMEC	breast
5	chr3:52187200-52188600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:52187200-52189400	Active TSS	Fetal Kidney	kidney
7	chr3:52187400-52188400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:52187400-52188400	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr3:52187400-52188400	Flanking Active TSS	Colonic Mucosa	Colon
10	chr3:52187400-52188400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr3:52187400-52188400	Flanking Active TSS	Fetal Muscle Leg	muscle
12	chr3:52187400-52188400	Flanking Active TSS	Fetal Thymus	thymus
13	chr3:52187400-52189400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr3:52187400-52189400	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr3:52187400-52189400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:52187600-52188400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr3:52187600-52188400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr3:52187600-52188400	Flanking Active TSS	Esophagus	oesophagus
19	chr3:52187600-52188400	Flanking Active TSS	Placenta	Placenta
20	chr3:52187600-52188400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr3:52187600-52188400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr3:52187600-52188400	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr3:52187600-52188400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr3:52187600-52189000	Active TSS	HepG2	liver
25	chr3:52187600-52189200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr3:52187600-52189200	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr3:52187600-52189400	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr3:52187600-52189400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:52187600-52189400	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr3:52187800-52188400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr3:52187800-52188400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr3:52187800-52188400	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr3:52187800-52188400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr3:52187800-52188400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr3:52187800-52188400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr3:52187800-52188400	Flanking Active TSS	Liver	Liver
37	chr3:52187800-52188400	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr3:52187800-52188400	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr3:52187800-52188400	Flanking Active TSS	Fetal Brain Female	brain
40	chr3:52187800-52188400	Flanking Active TSS	Pancreas	Pancrea
41	chr3:52187800-52188400	Flanking Active TSS	Right Ventricle	heart
42	chr3:52187800-52189000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52187800-52189000	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr3:52187800-52189000	Active TSS	Dnd41	blood
45	chr3:52187800-52189000	Active TSS	Hela-S3	cervix
46	chr3:52187800-52189200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:52187800-52189200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:52187800-52189200	Active TSS	NHDF-Ad	bronchial
49	chr3:52187800-52189400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:52187800-52189400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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