Variant report

Variant	rs566490
Chromosome Location	chr9:27204798-27204799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10757641	0.89[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs1178258	0.83[YRI][hapmap]
rs1319528	0.90[ASN][1000 genomes]
rs13286917	0.81[ASN][1000 genomes]
rs13295206	1.00[JPT][hapmap]
rs2181031	0.81[AFR][1000 genomes]
rs2224530	0.81[AMR][1000 genomes]
rs2273722	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2756900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3117638	0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs489451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs489552	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs536482	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs541065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs542913	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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs558931	0.88[AFR][1000 genomes]
rs574118	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];0.95[ASN][1000 genomes]
rs578327	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs590894	0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs591831	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs593621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594949	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];0.98[ASN][1000 genomes]
rs595303	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];0.95[ASN][1000 genomes]
rs607650	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];0.95[ASN][1000 genomes]
rs608416	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];0.95[ASN][1000 genomes]
rs608934	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs609766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs633903	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs638189	1.00[YRI][hapmap]
rs685421	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs685434	0.85[AFR][1000 genomes]
rs927370	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs927371	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv892864	chr9:27176554-27296705	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv466335	chr9:27179244-27234029	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv613946	chr9:27179244-27234029	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1027482	chr9:27195840-27233157	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1018864	chr9:27195840-27294815	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2761268	chr9:27195852-27291261	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv466336	chr9:27196119-27292703	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv471294	chr9:27196119-27292703	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv613947	chr9:27196119-27292703	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1033002	chr9:27199373-27232601	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region lncRNA	1 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	chr9:27151000-27229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:27165400-27219200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:27166200-27205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:27166200-27229000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:27180800-27230600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:27184200-27212600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:27193000-27204800	Weak transcription	Lung	lung
8	chr9:27193000-27209000	Weak transcription	Fetal Stomach	stomach
9	chr9:27193000-27212600	Weak transcription	Spleen	Spleen
10	chr9:27193000-27220000	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:27195200-27221800	Weak transcription	Fetal Intestine Large	intestine
12	chr9:27195400-27204800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:27196800-27228800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:27198400-27219800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr9:27198400-27219800	Weak transcription	Ovary	ovary
16	chr9:27201200-27212600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:27201400-27224800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:27202200-27205400	Strong transcription	HUVEC	blood vessel
19	chr9:27202400-27220600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:27203400-27205000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:27203600-27205000	Enhancers	HSMMtube	muscle
22	chr9:27203600-27205200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:27203600-27205200	Enhancers	HSMM	muscle
24	chr9:27203600-27205400	Enhancers	Osteobl	bone
25	chr9:27203800-27205000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:27203800-27205400	Enhancers	NHEK	skin
27	chr9:27203800-27205800	Weak transcription	Left Ventricle	heart
28	chr9:27203800-27218600	Weak transcription	Aorta	Aorta
29	chr9:27204000-27204800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:27204200-27204800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:27204400-27205200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:27204400-27205200	Enhancers	NH-A	brain
33	chr9:27204400-27205400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:27204600-27205000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:27204600-27207400	Strong transcription	Adipose Nuclei	Adipose

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