Variant report

Variant	rs12343517
Chromosome Location	chr9:117928708-117928709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10119433	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10122596	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10465110	0.83[JPT][hapmap]
rs10817717	0.83[JPT][hapmap]
rs10982592	0.86[JPT][hapmap]
rs12347472	0.81[YRI][hapmap]
rs12683537	0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12685855	0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1335346	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748164	0.81[ASN][1000 genomes]
rs3748165	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56883831	0.83[ASN][1000 genomes]
rs57178492	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57245991	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57262272	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57654109	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59797450	1.00[EUR][1000 genomes]
rs7030384	0.86[JPT][hapmap]
rs7031771	0.83[JPT][hapmap]
rs7048739	0.86[JPT][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	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
2	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
3	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv6681	chr9:117893926-117938609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117922000-117944600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:117926400-117928800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr9:117926400-117928800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:117926400-117931800	Enhancers	NHEK	skin
5	chr9:117926400-117933600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:117926600-117931600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:117927200-117929000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:117927200-117929400	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:117927200-117931600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:117927200-117931800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:117927200-117932200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:117927200-117933000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:117927200-117933000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:117927400-117929000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr9:117927400-117929200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr9:117927400-117929200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:117927400-117929200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:117927400-117929200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:117927400-117929200	Weak transcription	NH-A	brain
20	chr9:117927400-117929200	Weak transcription	Osteobl	bone
21	chr9:117927400-117929400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:117927400-117929600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:117927400-117929800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:117927400-117932000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:117927400-117933000	Weak transcription	A549	lung
26	chr9:117927600-117929200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr9:117927600-117929200	Weak transcription	NHLF	lung
28	chr9:117927600-117929400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:117927800-117929200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:117927800-117929200	Weak transcription	HMEC	breast
31	chr9:117927800-117929400	Weak transcription	HSMM	muscle
32	chr9:117927800-117929400	Weak transcription	HSMMtube	muscle
33	chr9:117928600-117930600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:117928600-117930600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:117928600-117930800	Enhancers	NHDF-Ad	bronchial

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