Variant report

Variant	rs12684773
Chromosome Location	chr9:104276211-104276212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10521057	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10819945	0.82[JPT][hapmap]
rs1113384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1124148	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12683273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12684621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685862	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12686025	0.87[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1407868	0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs16920420	0.81[JPT][hapmap]
rs16920438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16920439	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs16920447	0.81[JPT][hapmap]
rs16920479	0.84[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16920483	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16920504	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1929484	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150737	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4097641	0.91[JPT][hapmap]
rs45572636	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4742818	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4743465	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743471	0.86[CEU][hapmap];0.83[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56357103	0.82[ASN][1000 genomes]
rs56682764	0.82[ASN][1000 genomes]
rs57053192	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59111885	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59837044	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62575809	0.82[ASN][1000 genomes]
rs68067101	0.81[ASN][1000 genomes]
rs72743378	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72743387	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72743390	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72743392	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72743393	0.82[ASN][1000 genomes]
rs72743394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72743396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72743397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745315	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72745318	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7867496	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7873168	1.00[ASN][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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv893627	chr9:104268342-104334333	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 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	chr9:104272200-104276400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:104273400-104277400	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr9:104274000-104277200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:104274000-104277200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:104274000-104277200	Enhancers	Osteobl	bone
6	chr9:104274000-104277400	Enhancers	NHDF-Ad	bronchial
7	chr9:104274000-104277600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:104274000-104277600	Enhancers	NHLF	lung
9	chr9:104274000-104277800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr9:104274200-104277200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr9:104274200-104277200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:104274200-104277200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr9:104274600-104277200	Enhancers	HSMM	muscle
14	chr9:104274600-104277600	Enhancers	H9 Cell Line	embryonic stem cell
15	chr9:104275000-104276800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:104275000-104276800	Weak transcription	Pancreas	Pancrea
17	chr9:104275400-104277200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr9:104275400-104277400	Enhancers	Brain Anterior Caudate	brain
19	chr9:104275400-104277600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr9:104275600-104276400	Flanking Active TSS	Fetal Heart	heart
21	chr9:104275600-104277400	Enhancers	HSMMtube	muscle
22	chr9:104275800-104276400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr9:104275800-104277000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:104276000-104276400	Enhancers	Psoas Muscle	Psoas
25	chr9:104276000-104276400	Enhancers	Right Atrium	heart
26	chr9:104276000-104276600	Enhancers	Left Ventricle	heart
27	chr9:104276000-104276600	Enhancers	NHEK	skin
28	chr9:104276000-104276800	Weak transcription	Right Ventricle	heart
29	chr9:104276000-104277000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:104276000-104277000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:104276000-104277000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:104276000-104277000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:104276000-104277200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:104276000-104277200	Enhancers	Adipose Nuclei	Adipose
35	chr9:104276000-104277200	Enhancers	Fetal Muscle Leg	muscle
36	chr9:104276000-104277200	Enhancers	NH-A	brain
37	chr9:104276200-104276400	Enhancers	Aorta	Aorta
38	chr9:104276200-104276800	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr9:104276200-104277200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr9:104276200-104277600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr9:104276200-104286400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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