Variant report

Variant	rs289673
Chromosome Location	chr16:12430870-12430871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11075061	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11075062	0.82[CEU][hapmap]
rs11645864	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11648255	0.92[EUR][1000 genomes]
rs11648926	0.84[EUR][1000 genomes]
rs12102400	0.84[EUR][1000 genomes]
rs12102608	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12148953	0.80[EUR][1000 genomes]
rs12445263	0.80[EUR][1000 genomes]
rs12445569	0.84[EUR][1000 genomes]
rs12446650	0.81[EUR][1000 genomes]
rs12448443	0.82[EUR][1000 genomes]
rs158467	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16959318	0.87[EUR][1000 genomes]
rs176717	0.86[EUR][1000 genomes]
rs17697005	0.81[EUR][1000 genomes]
rs17764604	0.81[EUR][1000 genomes]
rs209834	0.84[EUR][1000 genomes]
rs209835	0.82[EUR][1000 genomes]
rs209839	0.82[EUR][1000 genomes]
rs209846	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209849	0.87[EUR][1000 genomes]
rs209850	0.87[EUR][1000 genomes]
rs209851	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs209853	0.89[EUR][1000 genomes]
rs209855	0.87[EUR][1000 genomes]
rs209856	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2856771	0.81[EUR][1000 genomes]
rs31679	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35818743	0.82[EUR][1000 genomes]
rs476267	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4780418	0.80[EUR][1000 genomes]
rs4780422	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4780423	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4781200	0.81[EUR][1000 genomes]
rs4781201	0.84[EUR][1000 genomes]
rs4781207	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4781208	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4781209	0.96[CEU][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs544598	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62039994	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6498278	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6498279	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7184477	0.90[EUR][1000 genomes]
rs7189386	0.81[EUR][1000 genomes]
rs7189945	0.83[EUR][1000 genomes]
rs7190509	0.96[CEU][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7194981	0.82[EUR][1000 genomes]
rs7195024	0.92[CEU][hapmap]
rs7195981	0.87[EUR][1000 genomes]
rs7199556	0.83[EUR][1000 genomes]
rs7201621	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs7204209	0.81[EUR][1000 genomes]
rs8046012	0.80[EUR][1000 genomes]
rs8051758	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs868773	0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs869289	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9284322	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9302469	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9939036	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1045385	chr16:12376389-12517006	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542748	chr16:12376389-12517006	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv905349	chr16:12408750-12445863	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv571464	chr16:12423557-12449778	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
2	chr16:12405600-12442400	Weak transcription	Spleen	Spleen
3	chr16:12410000-12456600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr16:12410200-12464800	Weak transcription	Gastric	stomach
5	chr16:12414400-12431400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr16:12414800-12432000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr16:12415000-12431600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr16:12415400-12435400	Weak transcription	Pancreas	Pancrea
9	chr16:12416800-12438600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr16:12418400-12433400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr16:12418400-12433400	Weak transcription	Brain Substantia Nigra	brain
12	chr16:12418400-12438400	Weak transcription	Brain Anterior Caudate	brain
13	chr16:12422000-12432200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr16:12423800-12433600	Weak transcription	HSMMtube	muscle
15	chr16:12425000-12435400	Weak transcription	Right Atrium	heart
16	chr16:12425200-12433600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr16:12425200-12433600	Weak transcription	Ovary	ovary
18	chr16:12425200-12442200	Weak transcription	Psoas Muscle	Psoas
19	chr16:12425400-12432000	Weak transcription	Adipose Nuclei	Adipose
20	chr16:12425400-12433200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr16:12425400-12433400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr16:12425400-12442000	Weak transcription	GM12878-XiMat	blood
23	chr16:12425600-12432400	Strong transcription	Primary B cells from cord blood	blood
24	chr16:12426800-12431600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr16:12426800-12433800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr16:12426800-12434800	Weak transcription	Fetal Muscle Leg	muscle
27	chr16:12426800-12447200	Weak transcription	Lung	lung
28	chr16:12427200-12432400	Enhancers	Fetal Heart	heart
29	chr16:12428200-12435400	Weak transcription	Primary T cells from cord blood	blood
30	chr16:12428400-12442400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr16:12428400-12461200	Weak transcription	Thymus	Thymus
32	chr16:12428800-12431000	Enhancers	Fetal Brain Male	brain
33	chr16:12428800-12432200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr16:12428800-12432400	Enhancers	Left Ventricle	heart
35	chr16:12429000-12433600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr16:12429200-12434000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr16:12430000-12435400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr16:12430200-12431000	Enhancers	Stomach Smooth Muscle	stomach
39	chr16:12430400-12433600	Weak transcription	Colon Smooth Muscle	Colon
40	chr16:12430400-12436600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr16:12430600-12435200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr16:12430800-12432200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr16:12430800-12432400	Enhancers	Right Ventricle	heart

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