Variant report

Variant	rs945258
Chromosome Location	chr9:117955913-117955914
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10739433	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10739434	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10759760	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817722	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10817728	0.86[CHB][hapmap]
rs1335340	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1335343	0.87[JPT][hapmap]
rs1335344	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1335345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1335351	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1335354	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1335355	0.86[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1335356	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1335360	0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs1360823	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1414138	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs1414148	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1414150	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1537731	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537733	0.86[CHB][hapmap]
rs1537734	0.86[CHB][hapmap]
rs1591421	0.82[JPT][hapmap]
rs1591422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1591423	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4978625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4978626	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4979508	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs4979511	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6478147	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6478150	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478151	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6478152	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478153	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7027442	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7027882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7031000	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7043594	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7043679	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7044001	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7044556	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7045288	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7045508	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7045599	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7357796	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7470092	0.86[EUR][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	chr9:117945600-117959400	Weak transcription	Fetal Kidney	kidney
3	chr9:117945800-117959600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:117954000-117956400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr9:117954000-117956800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr9:117954000-117956800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr9:117954000-117956800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr9:117954000-117956800	Enhancers	Fetal Muscle Leg	muscle
9	chr9:117954400-117957400	Enhancers	Colon Smooth Muscle	Colon
10	chr9:117954600-117957000	Enhancers	NHLF	lung
11	chr9:117954600-117957400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:117954600-117959400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:117954800-117956200	Enhancers	Fetal Lung	lung
14	chr9:117955000-117956600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr9:117955000-117957400	Enhancers	NHDF-Ad	bronchial
16	chr9:117955200-117956600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:117955200-117956800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr9:117955200-117957200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:117955200-117957200	Enhancers	Adipose Nuclei	Adipose
20	chr9:117955400-117956800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr9:117955400-117956800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr9:117955400-117957200	Enhancers	Osteobl	bone
23	chr9:117955600-117956600	Weak transcription	NH-A	brain
24	chr9:117955600-117957200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:117955600-117959000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:117955600-117959400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:117955600-117960200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:117955600-117960400	Weak transcription	Fetal Stomach	stomach
29	chr9:117955600-117960400	Weak transcription	Spleen	Spleen
30	chr9:117955600-117969000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr9:117955800-117956600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:117955800-117957000	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr9:117955800-117957400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:117955800-117960200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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