Variant report

Variant	rs9939080
Chromosome Location	chr16:75377514-75377515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10438605	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11149817	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12149472	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149940	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12444789	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445803	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12716785	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12918234	0.86[ASN][1000 genomes]
rs12919055	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12921808	1.00[ASN][1000 genomes]
rs12926447	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12928461	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12935491	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13337069	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13339257	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17605695	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17674216	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285221	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2550325	1.00[ASN][1000 genomes]
rs2550916	1.00[ASN][1000 genomes]
rs2650408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2650409	1.00[ASN][1000 genomes]
rs28368934	0.90[ASN][1000 genomes]
rs28510780	0.93[ASN][1000 genomes]
rs28525459	0.93[ASN][1000 genomes]
rs34532060	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35255668	0.81[EUR][1000 genomes]
rs4081763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383172	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55715607	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55719515	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59800961	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60544814	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6625	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71380715	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7184596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7185880	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7186825	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7188111	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7189037	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7206589	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206780	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs729109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8046261	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047147	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8047983	0.93[ASN][1000 genomes]
rs8048683	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050367	0.89[ASN][1000 genomes]
rs8051151	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051238	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052405	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052555	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054557	0.89[ASN][1000 genomes]
rs8055098	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8056345	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056473	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8057652	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8057925	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8059427	0.93[ASN][1000 genomes]
rs8059883	0.93[ASN][1000 genomes]
rs8060338	0.93[ASN][1000 genomes]
rs8063733	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9319483	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9319484	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9745455	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921115	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921330	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923034	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923465	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9923574	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924524	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926453	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9926933	0.93[ASN][1000 genomes]
rs9927330	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930002	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9932982	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9935954	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9935967	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936641	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936648	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936853	0.93[ASN][1000 genomes]
rs9937903	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9938936	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939587	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9940189	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940884	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941142	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972714	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	nsv833283	chr16:75302175-75392308	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2762265	chr16:75368897-75415866	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9939080	RP11-252K23.2	cis	Adipose Subcutaneous	GTEx
rs9939080	RP11-252K23.2	cis	Nerve Tibial	GTEx
rs9939080	RP11-252K23.2	cis	Esophagus Mucosa	GTEx
rs9939080	RP11-252K23.2	cis	Thyroid	GTEx
rs9939080	RP11-252K23.2	cis	Artery Tibial	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75338800-75426400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr16:75339400-75411800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr16:75342200-75381200	Weak transcription	Esophagus	oesophagus
4	chr16:75352200-75396000	Weak transcription	Lung	lung
5	chr16:75354800-75413600	Weak transcription	Fetal Thymus	thymus
6	chr16:75355400-75379800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:75358400-75421400	Weak transcription	K562	blood
8	chr16:75365200-75392400	Weak transcription	Brain Angular Gyrus	brain
9	chr16:75368600-75379600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr16:75368600-75396600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr16:75368600-75411400	Weak transcription	GM12878-XiMat	blood
12	chr16:75368600-75412800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr16:75368800-75409800	Weak transcription	Thymus	Thymus
14	chr16:75368800-75413200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr16:75369200-75406000	Weak transcription	Dnd41	blood
16	chr16:75371400-75381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr16:75371800-75378400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr16:75373000-75378600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr16:75373400-75378000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr16:75374000-75377800	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr16:75374000-75378000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr16:75374000-75378400	Enhancers	Fetal Kidney	kidney
23	chr16:75374200-75378400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr16:75374400-75377600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr16:75374400-75377600	Enhancers	HMEC	breast
26	chr16:75374400-75377800	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr16:75374400-75378200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr16:75374400-75378200	Enhancers	Fetal Lung	lung
29	chr16:75374400-75378200	Enhancers	Osteobl	bone
30	chr16:75374400-75378400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr16:75374400-75378600	Enhancers	Fetal Stomach	stomach
32	chr16:75374400-75380200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr16:75374600-75377600	Enhancers	HSMM	muscle
34	chr16:75374600-75377800	Enhancers	Small Intestine	intestine
35	chr16:75374600-75377800	Enhancers	NH-A	brain
36	chr16:75374600-75377800	Enhancers	NHEK	skin
37	chr16:75374600-75378000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr16:75374600-75378200	Enhancers	Fetal Brain Female	brain
39	chr16:75374600-75378400	Enhancers	Rectal Smooth Muscle	rectum
40	chr16:75374600-75378400	Enhancers	Stomach Smooth Muscle	stomach
41	chr16:75374600-75380800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr16:75374800-75377600	Enhancers	Liver	Liver
43	chr16:75374800-75377600	Enhancers	NHDF-Ad	bronchial
44	chr16:75374800-75377800	Enhancers	Colon Smooth Muscle	Colon
45	chr16:75374800-75377800	Enhancers	Fetal Muscle Leg	muscle
46	chr16:75374800-75378000	Enhancers	Fetal Heart	heart
47	chr16:75374800-75378200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr16:75374800-75378200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:75374800-75378200	Enhancers	NHLF	lung
50	chr16:75374800-75378400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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