Variant report

Variant	rs7622397
Chromosome Location	chr3:110923308-110923309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12185974	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1370	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1801650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1824709	0.89[EUR][1000 genomes]
rs56324569	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56724510	0.89[EUR][1000 genomes]
rs58112872	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61190717	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6437943	0.83[EUR][1000 genomes]
rs73852384	0.89[EUR][1000 genomes]
rs73852394	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73852397	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73852398	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73852399	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73852401	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73852402	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854903	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854905	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854910	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73854911	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854912	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854913	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854914	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854915	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854916	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854919	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854920	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73854921	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854922	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854923	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73854926	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854927	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615927	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7616280	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7642664	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9844779	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv829675	chr3:110885605-111101858	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877339	chr3:110889974-111070554	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv3945	chr3:110922029-110967244	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110835600-110929600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:110869400-110929000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:110881000-110928000	Weak transcription	Osteobl	bone
4	chr3:110894000-110924000	Weak transcription	Fetal Stomach	stomach
5	chr3:110894000-110934400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:110894200-110924800	Weak transcription	Fetal Intestine Small	intestine
7	chr3:110894200-110925600	Weak transcription	NHLF	lung
8	chr3:110894200-110929600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:110899200-110935200	Weak transcription	Lung	lung
10	chr3:110903400-110929200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:110910200-110927200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:110912000-110923800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:110913400-110924200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:110913400-110932000	Weak transcription	Fetal Heart	heart
15	chr3:110914200-110924000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:110914200-110925800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:110914400-110924200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:110914400-110924200	Weak transcription	Left Ventricle	heart
19	chr3:110914400-110928400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:110915000-110924000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:110915000-110934200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:110915400-110928000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:110915600-110929800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:110916000-110928200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:110916200-110925600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:110916400-110924400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:110916600-110923800	Weak transcription	Dnd41	blood
28	chr3:110916800-110923800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:110917000-110923400	Weak transcription	Liver	Liver
30	chr3:110917000-110933400	Weak transcription	Placenta	Placenta
31	chr3:110917200-110924200	Weak transcription	Fetal Lung	lung
32	chr3:110917200-110929000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:110917400-110923400	Weak transcription	Adipose Nuclei	Adipose
34	chr3:110917600-110928000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:110918400-110925000	Weak transcription	Pancreas	Pancrea
36	chr3:110919000-110923800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:110919400-110924000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:110919400-110928800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:110919400-110928800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:110919400-110929000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:110919400-110929000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:110919400-110929600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:110919600-110923600	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:110919600-110928800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:110920000-110945800	Weak transcription	HSMMtube	muscle
46	chr3:110922200-110924400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr3:110922400-110928400	Weak transcription	HSMM	muscle
48	chr3:110922600-110924200	Weak transcription	Fetal Intestine Large	intestine
49	chr3:110922600-110929000	Weak transcription	NHDF-Ad	bronchial
50	chr3:110922600-110933600	Weak transcription	Aorta	Aorta

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