Variant report

Variant	rs12238717
Chromosome Location	chr9:117869176-117869177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10817709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10817710	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10817711	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10982516	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10982518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10982519	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10982530	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10982531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10982532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10982538	1.00[ASN][1000 genomes]
rs10982539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10982545	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10982547	1.00[AMR][1000 genomes]
rs10982551	1.00[AMR][1000 genomes]
rs10982561	1.00[AMR][1000 genomes]
rs12235159	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12237691	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs12238613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3827815	0.94[ASN][1000 genomes]
rs56791225	1.00[AMR][1000 genomes]
rs57367241	1.00[AMR][1000 genomes]
rs59205962	1.00[AMR][1000 genomes]
rs59939445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60003319	1.00[AMR][1000 genomes]
rs60760004	1.00[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	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117849400-117876200	Weak transcription	Aorta	Aorta
2	chr9:117849400-117877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:117853400-117874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:117861600-117870400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:117861600-117876000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:117861800-117874800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:117862400-117872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:117862600-117877200	Weak transcription	Fetal Kidney	kidney
9	chr9:117862600-117877200	Weak transcription	Fetal Stomach	stomach
10	chr9:117864600-117870600	Enhancers	HMEC	breast
11	chr9:117865400-117870000	Enhancers	Colon Smooth Muscle	Colon
12	chr9:117865800-117870800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:117866400-117875000	Enhancers	Rectal Smooth Muscle	rectum
14	chr9:117866600-117870800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:117866800-117870400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:117867000-117869200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:117867000-117870400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr9:117867000-117870400	Enhancers	NH-A	brain
19	chr9:117867200-117870200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:117867400-117870800	Enhancers	Liver	Liver
21	chr9:117867400-117872200	Enhancers	NHEK	skin
22	chr9:117867400-117874000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:117867600-117869200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:117867600-117869200	Enhancers	Fetal Lung	lung
25	chr9:117867600-117869400	Enhancers	A549	lung
26	chr9:117867800-117870200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:117868000-117869400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:117868000-117870200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr9:117868400-117870400	Enhancers	Osteobl	bone
30	chr9:117868600-117869200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr9:117868800-117869200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:117868800-117869200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:117868800-117869200	Flanking Active TSS	NHDF-Ad	bronchial
34	chr9:117868800-117869400	Flanking Active TSS	NHLF	lung
35	chr9:117868800-117870200	Weak transcription	Stomach Mucosa	stomach
36	chr9:117868800-117871600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:117869000-117869200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:117869000-117869400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:117869000-117869800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:117869000-117876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr9:117869000-117876800	Weak transcription	HSMM	muscle

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