Variant report

Variant	rs6765133
Chromosome Location	chr3:110794998-110794999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:110794434-110795089	SK-N-SH	brain:	n/a	chr3:110794719-110794727 chr3:110794716-110794729
2	GATA3	chr3:110794364-110795106	SK-N-SH	brain:	n/a	chr3:110794719-110794727 chr3:110794716-110794729

Variant related genes	Relation type
PVRL3-AS1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10433385	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap]
rs10934073	0.96[EUR][1000 genomes]
rs12108091	0.81[ASN][1000 genomes]
rs12487779	0.85[ASN][1000 genomes]
rs12488066	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492309	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1351050	0.96[EUR][1000 genomes]
rs1381837	0.90[CHB][hapmap]
rs1477841	0.83[JPT][hapmap]
rs1477843	0.83[JPT][hapmap]
rs1477847	0.82[JPT][hapmap]
rs2126713	0.83[JPT][hapmap]
rs2399373	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4682229	0.83[JPT][hapmap]
rs4682230	0.83[JPT][hapmap]
rs4682231	0.83[JPT][hapmap]
rs4682234	0.83[JPT][hapmap]
rs61035297	0.88[AFR][1000 genomes]
rs6437948	0.83[JPT][hapmap]
rs6437956	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs72622317	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72935992	0.88[AFR][1000 genomes]
rs72935996	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72937909	0.81[AFR][1000 genomes]
rs7612667	0.83[JPT][hapmap]
rs7650020	0.85[AFR][1000 genomes]
rs7653595	0.83[JPT][hapmap]
rs9821335	0.83[JPT][hapmap]
rs9828899	0.83[JPT][hapmap]
rs9866028	0.83[JPT][hapmap]
rs9876350	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv1850918	chr3:110685181-110889974	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110792400-110795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:110792400-110795600	Weak transcription	Small Intestine	intestine
3	chr3:110792600-110800000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:110792600-110802200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:110792600-110803600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:110792800-110795000	Active TSS	Fetal Brain Female	brain
7	chr3:110793000-110796800	Enhancers	Liver	Liver
8	chr3:110793000-110798400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:110793000-110799200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:110793000-110799200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:110793000-110799400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:110793200-110796800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:110793200-110798800	Weak transcription	HSMM	muscle
14	chr3:110793200-110799400	Weak transcription	Fetal Kidney	kidney
15	chr3:110793200-110799800	Weak transcription	HSMMtube	muscle
16	chr3:110793400-110795000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr3:110793400-110796600	Enhancers	HepG2	liver
18	chr3:110793400-110797200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:110793400-110799800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:110793600-110795200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:110793600-110797400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:110794000-110795400	Weak transcription	Fetal Intestine Small	intestine
23	chr3:110794000-110795600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:110794000-110797000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:110794000-110798400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:110794200-110795000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:110794200-110796400	Weak transcription	NHLF	lung
28	chr3:110794200-110796800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:110794200-110797000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:110794200-110798400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:110794200-110798400	Weak transcription	HUVEC	blood vessel
32	chr3:110794200-110800800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr3:110794200-110801600	Weak transcription	Ovary	ovary
34	chr3:110794200-110802200	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr3:110794200-110809200	Weak transcription	Fetal Brain Male	brain
36	chr3:110794400-110796200	Weak transcription	Stomach Mucosa	stomach
37	chr3:110794400-110797000	Weak transcription	A549	lung
38	chr3:110794400-110797800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:110794400-110799400	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:110794400-110813600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:110794600-110795000	Weak transcription	Fetal Intestine Large	intestine
42	chr3:110794600-110795000	Enhancers	Stomach Smooth Muscle	stomach
43	chr3:110794600-110795200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:110794600-110797800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:110794800-110795000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:110794800-110795000	Enhancers	Brain Anterior Caudate	brain
47	chr3:110794800-110795000	Enhancers	Duodenum Mucosa	Duodenum
48	chr3:110794800-110795000	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr3:110794800-110795600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:110794800-110796000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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