Variant report

Variant	rs2856784
Chromosome Location	chr16:12645576-12645577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10492794	0.83[EUR][1000 genomes]
rs11640491	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11643978	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11645403	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11645654	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11645856	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11645899	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11647147	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12148951	0.87[EUR][1000 genomes]
rs12149441	0.87[EUR][1000 genomes]
rs1540279	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1614433	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1615250	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1616112	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1618096	0.81[EUR][1000 genomes]
rs1641873	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1641877	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1641879	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1641881	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1641889	0.83[ASN][1000 genomes]
rs1641890	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1641893	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17240735	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17819472	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794306	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1794307	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1794308	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1794309	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1794310	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1794312	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1794313	0.81[EUR][1000 genomes]
rs1794316	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1970769	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2006159	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213293	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2301217	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2301218	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2301219	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2865230	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2902959	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2902961	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3764301	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3975365	0.84[EUR][1000 genomes]
rs4390575	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4513084	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55779146	0.87[EUR][1000 genomes]
rs62026884	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62026887	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62026956	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62026957	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62028253	0.85[EUR][1000 genomes]
rs62028254	0.85[EUR][1000 genomes]
rs7187812	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7188575	0.88[EUR][1000 genomes]
rs7190533	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7191878	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7195739	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7197122	0.87[EUR][1000 genomes]
rs728583	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9788839	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1054084	chr16:12625727-12650247	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv431433	chr16:12628409-12654408	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1842867	chr16:12632286-12678721	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1040887	chr16:12632918-12650247	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv2751546	chr16:12635498-12674704	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1040358	chr16:12636982-12650247	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1050004	chr16:12641649-12654618	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv9348	chr16:12642414-12649190	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12613000-12670800	Weak transcription	Pancreas	Pancrea
2	chr16:12632800-12646600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr16:12632800-12663800	Weak transcription	Aorta	Aorta
4	chr16:12633000-12646600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr16:12633400-12654400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr16:12639400-12646800	Weak transcription	Brain Angular Gyrus	brain
7	chr16:12639400-12659000	Weak transcription	Lung	lung
8	chr16:12639600-12645800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr16:12640000-12647200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr16:12640600-12646000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr16:12641200-12646000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr16:12641200-12646600	Weak transcription	Brain Substantia Nigra	brain
13	chr16:12641200-12667000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr16:12641600-12646400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr16:12642000-12645600	Weak transcription	HSMMtube	muscle
16	chr16:12642000-12646600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr16:12642000-12662200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr16:12642200-12655000	Weak transcription	Spleen	Spleen
19	chr16:12642400-12653000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr16:12642800-12646600	Weak transcription	Brain Hippocampus Middle	brain
21	chr16:12643000-12659200	Weak transcription	Placenta	Placenta
22	chr16:12643200-12653000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr16:12643600-12646000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr16:12643600-12646200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr16:12643800-12645600	Weak transcription	Gastric	stomach
26	chr16:12644000-12645800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr16:12644000-12646200	Enhancers	Primary T cells from cord blood	blood
28	chr16:12644200-12646000	Enhancers	Primary B cells from peripheral blood	blood
29	chr16:12644200-12646000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr16:12644200-12646000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr16:12644200-12646200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr16:12644600-12646000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr16:12644600-12646400	Enhancers	Thymus	Thymus
34	chr16:12644600-12647400	Enhancers	Fetal Thymus	thymus
35	chr16:12644800-12646600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr16:12645000-12645600	Enhancers	Primary B cells from cord blood	blood
37	chr16:12645000-12646200	Enhancers	GM12878-XiMat	blood
38	chr16:12645200-12645600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr16:12645200-12646800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr16:12645200-12661600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr16:12645400-12646000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr16:12645400-12646000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr16:12645400-12646000	Weak transcription	Esophagus	oesophagus
44	chr16:12645400-12647400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links