Variant report

Variant	rs12442755
Chromosome Location	chr15:73591223-73591224
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1017808	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11072407	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072408	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072411	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072412	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072415	0.83[ASN][1000 genomes]
rs1119251	0.91[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11634045	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11636981	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11856537	0.89[ASW][hapmap];0.86[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap]
rs12439852	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12440576	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12591304	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12594776	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12901272	0.84[CHB][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1382782	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1564347	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs16957683	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1878940	0.83[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2061890	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2252725	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap]
rs2292915	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2415145	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2415146	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2660821	0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2660824	0.91[JPT][hapmap]
rs2680338	0.88[ASN][1000 genomes]
rs2680340	1.00[ASN][1000 genomes]
rs2680341	0.86[ASN][1000 genomes]
rs34456824	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34953385	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35348961	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35391014	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35608416	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35778649	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36072085	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3743496	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3784795	0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3859014	0.88[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3859015	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs472681	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs476846	0.83[ASN][1000 genomes]
rs4776631	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4777585	0.80[EUR][1000 genomes]
rs4777587	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs4777588	0.80[EUR][1000 genomes]
rs4777592	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs486267	0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs488156	0.81[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs489531	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap]
rs491742	0.81[ASN][1000 genomes]
rs492362	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs498005	0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs498868	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs519946	0.83[ASN][1000 genomes]
rs519970	0.83[ASN][1000 genomes]
rs520824	0.87[ASN][1000 genomes]
rs549253	0.87[ASN][1000 genomes]
rs559260	0.91[ASN][1000 genomes]
rs563076	0.90[ASN][1000 genomes]
rs564765	0.86[ASN][1000 genomes]
rs568435	0.83[ASN][1000 genomes]
rs569532	0.82[ASN][1000 genomes]
rs570001	0.94[ASN][1000 genomes]
rs573397	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs576813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59628124	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62015498	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495051	0.80[EUR][1000 genomes]
rs6495052	0.89[ASW][hapmap];0.86[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.80[EUR][1000 genomes]
rs6495053	0.89[ASW][hapmap];0.86[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.80[EUR][1000 genomes]
rs6495057	0.89[ASW][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap]
rs7168555	0.81[CEU][hapmap]
rs72741448	0.88[ASN][1000 genomes]
rs7495084	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs8039418	0.82[CHB][hapmap]
rs8043494	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs983067	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12442755	TBC1D21	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73536200-73602000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:73538000-73593400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:73552800-73598400	Weak transcription	Small Intestine	intestine
4	chr15:73560800-73597200	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr15:73563200-73598600	Weak transcription	Stomach Mucosa	stomach
6	chr15:73563600-73593600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:73566400-73597800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:73568600-73600800	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr15:73570200-73597000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:73570400-73597000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:73571200-73601400	Strong transcription	Fetal Stomach	stomach
12	chr15:73574000-73596800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:73576400-73594600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:73577800-73598200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr15:73579200-73598200	Weak transcription	Psoas Muscle	Psoas
16	chr15:73579800-73591400	Strong transcription	Rectal Smooth Muscle	rectum
17	chr15:73580400-73594400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:73581600-73598000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:73582000-73595200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr15:73582000-73598000	Weak transcription	Fetal Heart	heart
21	chr15:73582800-73596800	Strong transcription	Fetal Lung	lung
22	chr15:73583400-73597000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr15:73583400-73598400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:73584600-73598000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:73584800-73597000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:73585000-73599400	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:73585400-73597200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr15:73585400-73599600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:73585600-73591400	Strong transcription	Fetal Muscle Leg	muscle
30	chr15:73585600-73591600	Strong transcription	Aorta	Aorta
31	chr15:73585600-73591600	Strong transcription	Pancreas	Pancrea
32	chr15:73585600-73592000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr15:73585600-73597000	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr15:73585800-73591400	Strong transcription	Brain Cingulate Gyrus	brain
35	chr15:73586400-73593600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:73586800-73601200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr15:73587200-73592000	Strong transcription	Colonic Mucosa	Colon
38	chr15:73587200-73597000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:73587200-73597000	Strong transcription	Brain Angular Gyrus	brain
40	chr15:73587400-73591600	Strong transcription	Brain Hippocampus Middle	brain
41	chr15:73587400-73591600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:73587400-73592000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:73587400-73596600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:73587600-73591400	Strong transcription	Gastric	stomach
45	chr15:73587600-73591400	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr15:73587600-73591600	Strong transcription	Brain Substantia Nigra	brain
47	chr15:73587600-73591600	Strong transcription	Fetal Brain Female	brain
48	chr15:73587600-73592600	Strong transcription	Brain Germinal Matrix	brain
49	chr15:73587600-73597400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:73588000-73591600	Strong transcription	Brain Anterior Caudate	brain

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