Variant report

Variant	rs939741
Chromosome Location	chr3:90065791-90065792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 143 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs11128081	0.90[AFR][1000 genomes]
rs11915250	1.00[EUR][1000 genomes]
rs11917293	0.90[AFR][1000 genomes]
rs11918512	0.86[AFR][1000 genomes]
rs11920640	0.98[AFR][1000 genomes]
rs11924267	0.95[AFR][1000 genomes]
rs11928160	1.00[EUR][1000 genomes]
rs11928161	1.00[EUR][1000 genomes]
rs11928197	1.00[EUR][1000 genomes]
rs11929614	1.00[EUR][1000 genomes]
rs11929622	1.00[EUR][1000 genomes]
rs11929639	1.00[EUR][1000 genomes]
rs12106840	0.90[AFR][1000 genomes]
rs12107978	0.85[AFR][1000 genomes]
rs12107987	0.86[AFR][1000 genomes]
rs1402829	0.98[AFR][1000 genomes]
rs1402830	0.95[AFR][1000 genomes]
rs1402831	0.98[AFR][1000 genomes]
rs1521801	0.96[AFR][1000 genomes]
rs1521805	1.00[AFR][1000 genomes]
rs1915735	1.00[EUR][1000 genomes]
rs1915788	0.97[AFR][1000 genomes]
rs1996783	0.95[AFR][1000 genomes]
rs1996784	0.98[AFR][1000 genomes]
rs2204078	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2204079	0.95[AFR][1000 genomes]
rs34684257	1.00[EUR][1000 genomes]
rs55719953	0.93[AFR][1000 genomes]
rs55726199	0.98[AFR][1000 genomes]
rs55743058	1.00[EUR][1000 genomes]
rs55900084	1.00[EUR][1000 genomes]
rs56089352	1.00[EUR][1000 genomes]
rs56108378	1.00[EUR][1000 genomes]
rs56257056	0.98[AFR][1000 genomes]
rs56763170	1.00[EUR][1000 genomes]
rs56978342	1.00[EUR][1000 genomes]
rs57237979	0.98[AFR][1000 genomes]
rs57243284	1.00[EUR][1000 genomes]
rs57601270	1.00[EUR][1000 genomes]
rs58016519	1.00[EUR][1000 genomes]
rs58442773	0.95[AFR][1000 genomes]
rs58444511	0.95[AFR][1000 genomes]
rs58944054	0.93[AFR][1000 genomes]
rs58977999	0.98[AFR][1000 genomes]
rs59015121	1.00[EUR][1000 genomes]
rs59399871	1.00[EUR][1000 genomes]
rs60329202	1.00[EUR][1000 genomes]
rs60507817	1.00[EUR][1000 genomes]
rs6551442	1.00[EUR][1000 genomes]
rs6551443	1.00[EUR][1000 genomes]
rs6551449	0.95[AFR][1000 genomes]
rs6770945	0.98[AFR][1000 genomes]
rs6772724	0.95[AFR][1000 genomes]
rs6774114	1.00[EUR][1000 genomes]
rs6774428	1.00[EUR][1000 genomes]
rs6780268	0.89[AFR][1000 genomes]
rs6782153	0.94[AFR][1000 genomes]
rs6787044	0.94[AFR][1000 genomes]
rs6789752	0.90[AFR][1000 genomes]
rs6793888	0.98[AFR][1000 genomes]
rs6798157	1.00[EUR][1000 genomes]
rs6798554	0.95[AFR][1000 genomes]
rs6800191	0.96[AFR][1000 genomes]
rs6800705	0.83[AFR][1000 genomes]
rs6801082	1.00[EUR][1000 genomes]
rs6804358	0.95[AFR][1000 genomes]
rs6807535	1.00[EUR][1000 genomes]
rs6807901	1.00[EUR][1000 genomes]
rs72915828	1.00[EUR][1000 genomes]
rs72915840	1.00[EUR][1000 genomes]
rs72915842	1.00[EUR][1000 genomes]
rs72915844	1.00[EUR][1000 genomes]
rs72917631	1.00[EUR][1000 genomes]
rs72917640	1.00[EUR][1000 genomes]
rs72917652	1.00[EUR][1000 genomes]
rs72917689	1.00[EUR][1000 genomes]
rs72921836	0.93[AFR][1000 genomes]
rs72921847	1.00[AFR][1000 genomes]
rs72921850	1.00[AFR][1000 genomes]
rs72921853	1.00[AFR][1000 genomes]
rs72921855	0.97[AFR][1000 genomes]
rs72921864	0.98[AFR][1000 genomes]
rs72921866	0.92[AFR][1000 genomes]
rs72921873	0.95[AFR][1000 genomes]
rs72921876	0.95[AFR][1000 genomes]
rs72923735	0.98[AFR][1000 genomes]
rs72923736	0.95[AFR][1000 genomes]
rs72923737	0.95[AFR][1000 genomes]
rs72923739	0.95[AFR][1000 genomes]
rs72923741	0.95[AFR][1000 genomes]
rs72923755	0.98[AFR][1000 genomes]
rs72923757	0.95[AFR][1000 genomes]
rs72923762	0.95[AFR][1000 genomes]
rs72923764	0.95[AFR][1000 genomes]
rs72923765	0.93[AFR][1000 genomes]
rs72923767	0.95[AFR][1000 genomes]
rs72923768	0.83[AFR][1000 genomes]
rs72923770	0.98[AFR][1000 genomes]
rs72923771	0.95[AFR][1000 genomes]
rs72923776	0.94[AFR][1000 genomes]
rs72923777	0.91[AFR][1000 genomes]
rs72923779	0.91[AFR][1000 genomes]
rs72923781	0.94[AFR][1000 genomes]
rs72923783	0.88[AFR][1000 genomes]
rs72923784	0.90[AFR][1000 genomes]
rs72923786	0.88[AFR][1000 genomes]
rs72923794	0.85[AFR][1000 genomes]
rs73846008	0.94[AFR][1000 genomes]
rs73847937	1.00[EUR][1000 genomes]
rs73849912	0.95[AFR][1000 genomes]
rs7610460	1.00[EUR][1000 genomes]
rs7610765	1.00[AFR][1000 genomes]
rs7619437	0.95[AFR][1000 genomes]
rs7626330	0.88[AFR][1000 genomes]
rs7627792	1.00[AFR][1000 genomes]
rs7637541	1.00[AFR][1000 genomes]
rs7648089	0.88[AFR][1000 genomes]
rs7648275	0.88[AFR][1000 genomes]
rs7648900	0.97[AFR][1000 genomes]
rs9714298	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1010932	chr3:89424428-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1010021	chr3:89521983-90141988	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv530024	chr3:89548440-90304841	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv869889	chr3:89653238-90087372	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1008130	chr3:89837442-90192503	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1010796	chr3:89870548-90192503	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1013598	chr3:89879377-90192503	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv536642	chr3:89879377-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv590966	chr3:89904882-90199759	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1007523	chr3:89951855-90144385	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1011581	chr3:89951855-90144746	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv997583	chr3:89951855-90154534	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1006665	chr3:89958844-90162193	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv998541	chr3:89961515-90153365	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv536643	chr3:89961515-90153365	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv590967	chr3:89979895-90138312	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv590968	chr3:89979895-90199759	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv460761	chr3:89987871-90138312	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv590969	chr3:89987871-90138312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv590970	chr3:89987871-90441306	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv1010292	chr3:90057464-90192503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:90060400-90065800	Weak transcription	Aorta	Aorta
2	chr3:90060400-90074200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:90060600-90065800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:90061000-90065800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:90064200-90066200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:90064200-90066200	Enhancers	HSMM	muscle
7	chr3:90064200-90066400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:90064400-90066000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:90064400-90066000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:90064400-90066000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:90064400-90066200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:90064400-90066200	Enhancers	Dnd41	blood
13	chr3:90064400-90066200	Enhancers	Hela-S3	cervix
14	chr3:90064400-90066200	Enhancers	HSMMtube	muscle
15	chr3:90064400-90066600	Enhancers	HMEC	breast
16	chr3:90064600-90066000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:90064600-90066000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:90064600-90066000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:90064600-90066000	Enhancers	Adipose Nuclei	Adipose
20	chr3:90064600-90066200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:90064600-90066200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:90064600-90066200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr3:90064600-90066200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:90064600-90066200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:90064600-90066200	Enhancers	NH-A	brain
26	chr3:90064600-90066200	Enhancers	Osteobl	bone
27	chr3:90064800-90066000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:90064800-90066000	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr3:90064800-90066200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:90064800-90066200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:90065000-90066200	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:90065000-90066200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:90065200-90066200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:90065200-90066200	Enhancers	Fetal Muscle Leg	muscle
35	chr3:90065400-90066200	Enhancers	Ovary	ovary
36	chr3:90065400-90066200	Enhancers	NHLF	lung
37	chr3:90065400-90066400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:90065400-90066600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:90065400-90066600	Enhancers	NHDF-Ad	bronchial
40	chr3:90065600-90066000	Enhancers	Fetal Muscle Trunk	muscle
41	chr3:90065600-90066200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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