Variant report

Variant	rs41271405
Chromosome Location	chr3:120129860-120129861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs55640624	1.00[EUR][1000 genomes]
rs55885326	1.00[EUR][1000 genomes]
rs56239327	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56281929	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56384860	1.00[EUR][1000 genomes]
rs58174591	1.00[EUR][1000 genomes]
rs58296615	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58932850	1.00[EUR][1000 genomes]
rs59522791	1.00[EUR][1000 genomes]
rs59766787	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59779647	1.00[EUR][1000 genomes]
rs60136263	1.00[EUR][1000 genomes]
rs60814807	1.00[EUR][1000 genomes]
rs61160321	1.00[EUR][1000 genomes]
rs61535593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6764372	1.00[EUR][1000 genomes]
rs72956841	0.85[AMR][1000 genomes]
rs72956853	1.00[EUR][1000 genomes]
rs72956859	1.00[EUR][1000 genomes]
rs72956861	1.00[EUR][1000 genomes]
rs72956897	1.00[EUR][1000 genomes]
rs72958712	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958714	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958778	1.00[EUR][1000 genomes]
rs73855206	1.00[EUR][1000 genomes]
rs73855223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73855241	1.00[EUR][1000 genomes]
rs73856465	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73856468	1.00[EUR][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120112000-120132600	Strong transcription	Placenta Amnion	Placenta Amnion
2	chr3:120112200-120130000	Strong transcription	Fetal Muscle Trunk	muscle
3	chr3:120112200-120131400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:120112200-120132600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:120112400-120130200	Strong transcription	Adipose Nuclei	Adipose
6	chr3:120112400-120132600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:120112400-120132600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:120112400-120132600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:120112400-120132600	Strong transcription	HSMMtube	muscle
10	chr3:120112400-120132600	Strong transcription	NH-A	brain
11	chr3:120112400-120132600	Strong transcription	NHDF-Ad	bronchial
12	chr3:120112400-120132600	Strong transcription	NHLF	lung
13	chr3:120112600-120130600	Strong transcription	Ovary	ovary
14	chr3:120112600-120131400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:120112600-120132400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:120112600-120132400	Strong transcription	Aorta	Aorta
17	chr3:120112600-120132600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:120112600-120132600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:120112600-120132800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:120112800-120131200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:120112800-120132000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:120112800-120132600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:120112800-120132600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:120113200-120132400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:120113200-120132600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:120113200-120132600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:120113200-120132600	Strong transcription	Fetal Kidney	kidney
28	chr3:120113200-120132600	Strong transcription	HUVEC	blood vessel
29	chr3:120113200-120133000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:120113400-120132400	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr3:120113400-120132600	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr3:120113400-120132600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:120113800-120132600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:120114000-120132400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:120114400-120132600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:120114400-120132800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:120114400-120143200	Weak transcription	Small Intestine	intestine
38	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:120118800-120135600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:120122200-120136000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:120122400-120135000	Weak transcription	Psoas Muscle	Psoas
42	chr3:120122400-120135800	Weak transcription	A549	lung
43	chr3:120123400-120131400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:120123400-120131600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:120123600-120131200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:120124200-120132400	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr3:120124200-120132600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:120124200-120132600	Strong transcription	Osteobl	bone
49	chr3:120125000-120131400	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:120125000-120132800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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