Variant report

Variant	rs2088285
Chromosome Location	chr16:65104342-65104343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1025311	0.80[JPT][hapmap]
rs1040270	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1040271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10500508	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1079008	0.93[JPT][hapmap]
rs12935138	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1356823	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1520229	0.87[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap]
rs1520230	0.87[JPT][hapmap];0.82[YRI][hapmap]
rs1520231	0.93[JPT][hapmap]
rs1520232	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1520234	0.87[JPT][hapmap]
rs1520236	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1520243	0.87[JPT][hapmap]
rs1532418	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs16968461	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs16968480	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs1915117	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2132543	0.90[ASN][1000 genomes]
rs2280396	0.81[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs257335	0.87[JPT][hapmap]
rs257336	0.87[JPT][hapmap]
rs257337	0.87[JPT][hapmap]
rs257341	0.80[JPT][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs257490	0.87[JPT][hapmap];0.83[MKK][hapmap]
rs257497	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs257498	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs28216	0.94[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs34553411	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35054335	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35140	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs35144	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs35146	0.80[JPT][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs35148	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs35149	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs35150	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs35152	0.82[YRI][hapmap]
rs35154	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs35176	0.81[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs35188	0.80[JPT][hapmap]
rs35191	0.80[JPT][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap]
rs35195	0.80[JPT][hapmap]
rs35198	0.80[JPT][hapmap];0.83[MKK][hapmap]
rs35199	0.80[JPT][hapmap];0.81[LWK][hapmap]
rs35200	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs35203	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs35204	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs35208	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs35209	1.00[YRI][hapmap]
rs35210	0.80[JPT][hapmap];0.82[YRI][hapmap]
rs35214	0.80[JPT][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs35216	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs35219	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs35709707	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40115	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs40116	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs42863	0.80[JPT][hapmap]
rs4393595	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4967866	0.80[JPT][hapmap]
rs4967868	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4967882	0.87[JPT][hapmap]
rs4967884	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4967885	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4967886	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7204729	0.87[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs7498801	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs8048351	0.98[ASN][1000 genomes]
rs878359	0.87[JPT][hapmap]
rs909003	0.80[JPT][hapmap]
rs973200	0.80[JPT][hapmap]
rs974782	0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9935608	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948640	chr16:64859061-65112790	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv833260	chr16:65050647-65218759	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1831	chr16:65071976-65106105	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2088285	FAM96B	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:65058600-65104400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:65069800-65105000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr16:65087400-65104800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr16:65095000-65113400	Weak transcription	Lung	lung
5	chr16:65095800-65152000	Weak transcription	Fetal Intestine Large	intestine
6	chr16:65096200-65104800	Weak transcription	Fetal Kidney	kidney
7	chr16:65098800-65105000	Enhancers	Ovary	ovary
8	chr16:65100600-65104600	Enhancers	Brain Substantia Nigra	brain
9	chr16:65100600-65104800	Enhancers	Brain Cingulate Gyrus	brain
10	chr16:65100800-65104400	Enhancers	Brain Hippocampus Middle	brain
11	chr16:65100800-65104600	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr16:65100800-65104800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr16:65101400-65104400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr16:65101400-65104400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr16:65101400-65104800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr16:65101400-65104800	Weak transcription	Fetal Brain Female	brain
17	chr16:65101600-65104800	Enhancers	Brain Anterior Caudate	brain
18	chr16:65101600-65104800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr16:65101600-65104800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr16:65101600-65105400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr16:65101800-65105000	Enhancers	NHLF	lung
22	chr16:65102000-65104800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr16:65102000-65104800	Enhancers	HSMMtube	muscle
24	chr16:65102000-65105000	Enhancers	NHDF-Ad	bronchial
25	chr16:65102600-65104800	Weak transcription	Fetal Stomach	stomach
26	chr16:65103000-65104400	Weak transcription	Fetal Heart	heart
27	chr16:65103000-65104400	Enhancers	NH-A	brain
28	chr16:65103000-65104600	Enhancers	Stomach Smooth Muscle	stomach
29	chr16:65103000-65104600	Enhancers	A549	lung
30	chr16:65103000-65105600	Enhancers	HUVEC	blood vessel
31	chr16:65103000-65105800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr16:65103200-65104400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr16:65103200-65104800	Enhancers	Fetal Muscle Leg	muscle
34	chr16:65103400-65104400	Enhancers	Psoas Muscle	Psoas
35	chr16:65103400-65104600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr16:65103400-65104600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr16:65103400-65105800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr16:65103600-65104600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr16:65103600-65104600	Enhancers	Brain Angular Gyrus	brain
40	chr16:65103600-65104800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr16:65103600-65105000	Enhancers	Aorta	Aorta
42	chr16:65103600-65105400	Enhancers	HMEC	breast
43	chr16:65103600-65105600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr16:65103600-65105800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr16:65103800-65104400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr16:65103800-65104400	Enhancers	Spleen	Spleen
47	chr16:65103800-65104800	Enhancers	Adipose Nuclei	Adipose
48	chr16:65103800-65104800	Weak transcription	Brain Germinal Matrix	brain
49	chr16:65103800-65105600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr16:65103800-65108200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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