Variant report

Variant	rs4682229
Chromosome Location	chr3:110793652-110793653
allele	G/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	CEBPB	chr3:110793490-110793734	A549	lung:	n/a	chr3:110793640-110793651

Variant related genes	Relation type
PVRL3	TF binding region
PVRL3-AS1	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11717706	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11919892	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11929280	0.85[CEU][hapmap]
rs12492309	0.83[JPT][hapmap]
rs13060876	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13061640	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072462	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1381836	0.85[CEU][hapmap]
rs1382075	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1477841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1477842	1.00[CEU][hapmap];0.87[YRI][hapmap];0.80[AMR][1000 genomes]
rs1477843	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1477846	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1477847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1477848	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1477850	0.85[CEU][hapmap]
rs1477851	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs1477854	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1477855	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1547518	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1585629	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1600059	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16857350	0.85[CEU][hapmap]
rs1871026	0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2126710	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2126711	0.91[EUR][1000 genomes]
rs2126712	0.91[EUR][1000 genomes]
rs2126713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2169643	0.85[CEU][hapmap]
rs2399373	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399375	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4682033	0.81[AFR][1000 genomes]
rs4682230	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4682238	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs55774570	0.81[AFR][1000 genomes]
rs56668317	0.81[AFR][1000 genomes]
rs6437947	0.88[AFR][1000 genomes]
rs6437948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6437952	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6437953	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap]
rs6763050	0.85[CEU][hapmap]
rs6765133	0.83[JPT][hapmap]
rs6765948	0.83[EUR][1000 genomes]
rs6781480	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6790828	0.84[AFR][1000 genomes]
rs6794645	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7430600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7433877	0.85[CEU][hapmap]
rs7610760	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs7612572	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7612667	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7623880	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs7632375	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7632388	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7648752	0.82[CEU][hapmap]
rs7653595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs873132	0.85[CEU][hapmap]
rs9288918	0.85[CEU][hapmap]
rs969940	0.85[CEU][hapmap]
rs9817950	0.82[AFR][1000 genomes]
rs9818950	0.91[EUR][1000 genomes]
rs9821335	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828899	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837377	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9847598	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9866028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9876350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877855	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9882945	0.85[CEU][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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110788600-110794200	Active TSS	Ovary	ovary
2	chr3:110788600-110794600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:110788800-110794000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr3:110789000-110793800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:110789000-110794200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:110789200-110794200	Active TSS	NHLF	lung
7	chr3:110789200-110794800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:110789400-110794000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:110789600-110794800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:110791800-110794200	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr3:110792200-110794200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:110792200-110794400	Active TSS	Duodenum Mucosa	Duodenum
13	chr3:110792200-110794800	Flanking Active TSS	Dnd41	blood
14	chr3:110792400-110794000	Enhancers	Brain Hippocampus Middle	brain
15	chr3:110792400-110795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:110792400-110795600	Weak transcription	Small Intestine	intestine
17	chr3:110792600-110793800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:110792600-110794200	Active TSS	NH-A	brain
19	chr3:110792600-110800000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:110792600-110802200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:110792600-110803600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:110792800-110794000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:110792800-110794000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr3:110792800-110794000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:110792800-110794200	Weak transcription	Brain Anterior Caudate	brain
26	chr3:110792800-110794200	Enhancers	Fetal Heart	heart
27	chr3:110792800-110795000	Active TSS	Fetal Brain Female	brain
28	chr3:110793000-110793800	Weak transcription	Brain Angular Gyrus	brain
29	chr3:110793000-110793800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:110793000-110794400	Enhancers	Colon Smooth Muscle	Colon
31	chr3:110793000-110794800	Enhancers	Rectal Smooth Muscle	rectum
32	chr3:110793000-110796800	Enhancers	Liver	Liver
33	chr3:110793000-110798400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:110793000-110799200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr3:110793000-110799200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:110793000-110799400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:110793200-110793800	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:110793200-110793800	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr3:110793200-110793800	Enhancers	Fetal Brain Male	brain
40	chr3:110793200-110793800	Weak transcription	Fetal Intestine Small	intestine
41	chr3:110793200-110793800	Weak transcription	Stomach Mucosa	stomach
42	chr3:110793200-110793800	Enhancers	A549	lung
43	chr3:110793200-110794200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:110793200-110794200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr3:110793200-110794600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:110793200-110794800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr3:110793200-110796800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:110793200-110798800	Weak transcription	HSMM	muscle
49	chr3:110793200-110799400	Weak transcription	Fetal Kidney	kidney
50	chr3:110793200-110799800	Weak transcription	HSMMtube	muscle

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