Variant report

Variant	rs1888673
Chromosome Location	chr9:117962004-117962005
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10982595	0.90[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10982604	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982606	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10982609	0.91[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10982614	1.00[YRI][hapmap]
rs10982616	1.00[YRI][hapmap]
rs1110169	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379021	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12682693	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13292941	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1537732	0.86[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17244791	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888672	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183702	0.81[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34541555	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147052	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4978628	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478145	0.86[CEU][hapmap];0.93[CHB][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6478149	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7860900	0.86[CEU][hapmap];0.93[CHB][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7866181	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv893769	chr9:117936903-117985886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117930000-117964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:117955600-117969000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:117957000-117962800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:117959400-117968600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:117960600-117962600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:117960600-117962600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:117960600-117962800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:117960600-117963200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:117960600-117964400	Weak transcription	Fetal Muscle Leg	muscle
10	chr9:117960600-117964600	Weak transcription	NH-A	brain
11	chr9:117960600-117967400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:117960600-117969000	Weak transcription	Spleen	Spleen
13	chr9:117960800-117962200	Weak transcription	NHDF-Ad	bronchial
14	chr9:117960800-117962400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:117960800-117962400	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:117960800-117962800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:117960800-117963000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:117960800-117963000	Weak transcription	HMEC	breast
19	chr9:117960800-117963000	Weak transcription	HSMM	muscle
20	chr9:117960800-117963000	Weak transcription	NHEK	skin
21	chr9:117960800-117963000	Weak transcription	Osteobl	bone
22	chr9:117960800-117963200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:117960800-117963200	Weak transcription	NHLF	lung
24	chr9:117960800-117963400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:117960800-117964600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:117960800-117964600	Weak transcription	Fetal Stomach	stomach
27	chr9:117960800-117965000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:117960800-117968800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:117960800-117969400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:117960800-117975800	Weak transcription	Fetal Kidney	kidney
31	chr9:117961000-117963000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:117961600-117962400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:117961600-117965600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:117962000-117962400	Enhancers	Fetal Lung	lung

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