Variant report

Variant	rs56961588
Chromosome Location	chr9:117790602-117790603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10117421	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336431	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342978	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330361	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1537011	0.84[AMR][1000 genomes]
rs17239323	1.00[ASN][1000 genomes]
rs17241078	0.81[AMR][1000 genomes]
rs17241442	0.86[AMR][1000 genomes]
rs17817489	1.00[ASN][1000 genomes]
rs17819299	0.84[AMR][1000 genomes]
rs2001357	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2150101	0.84[AMR][1000 genomes]
rs28393206	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4549855	0.86[AMR][1000 genomes]
rs57398199	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578424	0.81[AMR][1000 genomes]
rs62578425	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv1840787	chr9:117787173-117803882	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv1826575	chr9:117787173-117805719	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117773400-117803200	Weak transcription	Esophagus	oesophagus
2	chr9:117776800-117791600	Weak transcription	Fetal Lung	lung
3	chr9:117781800-117791600	Weak transcription	Aorta	Aorta
4	chr9:117781800-117797400	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:117781800-117798200	Weak transcription	Fetal Intestine Large	intestine
6	chr9:117781800-117798400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:117781800-117808600	Weak transcription	Fetal Intestine Small	intestine
8	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
9	chr9:117783200-117792400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr9:117783200-117796800	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:117784400-117791600	Weak transcription	Fetal Kidney	kidney
12	chr9:117786200-117791400	Weak transcription	HSMM	muscle
13	chr9:117786200-117794800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:117786400-117794800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:117786600-117796600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:117786800-117791400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:117786800-117792600	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:117787600-117792400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr9:117787800-117791400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr9:117788000-117791600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:117788000-117796600	Strong transcription	NH-A	brain
22	chr9:117788200-117791000	Weak transcription	NHEK	skin
23	chr9:117788200-117791400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:117788200-117794600	Strong transcription	Colon Smooth Muscle	Colon
25	chr9:117788200-117794800	Strong transcription	Osteobl	bone
26	chr9:117788400-117790800	Weak transcription	HMEC	breast
27	chr9:117788400-117791800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:117788400-117795000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr9:117788400-117797400	Weak transcription	Spleen	Spleen
30	chr9:117788600-117791400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:117788600-117791800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:117788800-117796600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:117789000-117791200	Weak transcription	NHLF	lung
34	chr9:117789000-117791600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:117789000-117792400	Weak transcription	Lung	lung
36	chr9:117789000-117792600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:117789000-117808600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:117789400-117790800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:117789600-117791600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:117789600-117797400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr9:117789800-117791600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:117789800-117797400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:117790000-117791600	Weak transcription	Fetal Stomach	stomach
44	chr9:117790000-117797400	Strong transcription	NHDF-Ad	bronchial
45	chr9:117790200-117790800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:117790200-117796200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr9:117790400-117791400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr9:117790600-117790800	Strong transcription	Rectal Smooth Muscle	rectum

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