Variant report

Variant	rs16862886
Chromosome Location	chr1:169952327-169952328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10158922	1.00[AMR][1000 genomes]
rs10218486	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10919276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919288	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919294	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919295	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919296	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919300	1.00[EUR][1000 genomes]
rs10919308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12025296	1.00[EUR][1000 genomes]
rs12044536	1.00[EUR][1000 genomes]
rs12061373	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12061500	1.00[AMR][1000 genomes]
rs12061626	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066551	1.00[EUR][1000 genomes]
rs12071325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12076018	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12077685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12077708	1.00[EUR][1000 genomes]
rs12079608	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084420	1.00[AMR][1000 genomes]
rs12087450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12090220	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12091389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12095784	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13375701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16862978	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2103641	1.00[EUR][1000 genomes]
rs2272912	1.00[EUR][1000 genomes]
rs2901261	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4279900	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57038529	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023529	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023593	1.00[EUR][1000 genomes]
rs73041148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73041149	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74122312	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74122421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74122422	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74122452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7531947	1.00[EUR][1000 genomes]
rs989054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1013271	chr1:169892661-169960549	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv997289	chr1:169899427-169960549	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1012520	chr1:169899427-169969444	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1001670	chr1:169901733-169956450	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1004999	chr1:169901733-169960549	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1005982	chr1:169913597-169958219	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1001013	chr1:169913597-169960549	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1008890	chr1:169917450-169956450	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1009789	chr1:169917450-169960549	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1010370	chr1:169917450-169980951	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1012534	chr1:169924759-169965106	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169904000-170010400	Weak transcription	Aorta	Aorta
2	chr1:169911800-169968400	Weak transcription	Psoas Muscle	Psoas
3	chr1:169912000-169953600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:169912000-169966000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:169912000-169968600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:169912800-169967200	Weak transcription	NHDF-Ad	bronchial
7	chr1:169913400-169953600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:169913800-169968400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:169914000-169968400	Weak transcription	Ovary	ovary
10	chr1:169914600-169961800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:169914600-169968000	Weak transcription	Fetal Stomach	stomach
12	chr1:169914800-169984000	Weak transcription	Left Ventricle	heart
13	chr1:169914800-169984800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:169914800-169988800	Weak transcription	Fetal Intestine Small	intestine
15	chr1:169921600-169968400	Weak transcription	Fetal Brain Male	brain
16	chr1:169922000-169984000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:169922200-169968400	Weak transcription	Brain Angular Gyrus	brain
18	chr1:169922400-169996400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:169930400-169968400	Weak transcription	Small Intestine	intestine
20	chr1:169930800-169954200	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:169934800-169952800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:169935400-169954200	Weak transcription	Fetal Heart	heart
23	chr1:169935600-169968400	Weak transcription	Fetal Kidney	kidney
24	chr1:169937600-169956600	Weak transcription	Pancreas	Pancrea
25	chr1:169938000-169968400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:169938200-169965400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:169938600-169953400	Weak transcription	Right Ventricle	heart
28	chr1:169938800-169962200	Weak transcription	Esophagus	oesophagus
29	chr1:169939000-169968400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:169939200-169967400	Weak transcription	Osteobl	bone
31	chr1:169942000-169953400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:169944800-169954600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:169944800-169968000	Weak transcription	Brain Substantia Nigra	brain
34	chr1:169944800-169989600	Weak transcription	Thymus	Thymus
35	chr1:169945000-169953800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:169945200-169952400	Weak transcription	Brain Germinal Matrix	brain
37	chr1:169945200-169953000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr1:169945400-169968400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:169945800-169975000	Weak transcription	GM12878-XiMat	blood
40	chr1:169946000-169952800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:169946400-169968400	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:169947000-169968000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:169947200-169968000	Weak transcription	Brain Anterior Caudate	brain
44	chr1:169947800-169953800	Weak transcription	HMEC	breast
45	chr1:169948200-169959800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:169948600-169952600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:169948800-169952800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:169948800-169953400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:169948800-169968200	Weak transcription	HSMMtube	muscle
50	chr1:169949200-169952400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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