Variant report

Variant	rs11072411
Chromosome Location	chr15:73578528-73578529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1017808	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10518997	1.00[YRI][hapmap]
rs11072405	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11072407	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072408	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072412	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1119251	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11634045	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11636981	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11856537	1.00[ASW][hapmap];0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap]
rs12439852	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440576	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12442755	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]
rs12591304	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594776	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901272	0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12901649	0.80[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs12912737	0.81[ASN][1000 genomes]
rs1382782	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1564347	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1585766	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs16957683	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1878940	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1904335	0.80[ASN][1000 genomes]
rs2061890	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2252725	0.91[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2292915	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2415145	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2415146	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2660821	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2680338	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2680340	0.90[ASN][1000 genomes]
rs2680341	0.95[ASN][1000 genomes]
rs34456824	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34953385	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35348961	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35391014	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35608416	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35778649	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36072085	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3743496	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3784795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3859014	0.88[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3859015	0.89[ASW][hapmap];0.91[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs472681	0.90[ASN][1000 genomes]
rs4776631	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4777585	0.80[EUR][1000 genomes]
rs4777587	0.86[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs4777588	0.80[EUR][1000 genomes]
rs4777592	0.86[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs486267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs488156	0.88[CHD][hapmap]
rs489531	0.91[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs498005	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs520824	0.95[ASN][1000 genomes]
rs549253	0.96[ASN][1000 genomes]
rs559260	0.99[ASN][1000 genomes]
rs563076	0.99[ASN][1000 genomes]
rs564765	0.94[ASN][1000 genomes]
rs570001	0.86[ASN][1000 genomes]
rs576813	0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs59628124	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62015498	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495051	0.80[EUR][1000 genomes]
rs6495052	1.00[ASW][hapmap];0.86[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.80[EUR][1000 genomes]
rs6495053	1.00[ASW][hapmap];0.86[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.80[EUR][1000 genomes]
rs6495057	1.00[ASW][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap]
rs7168555	0.81[CEU][hapmap]
rs7177758	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs72741448	0.82[ASN][1000 genomes]
rs7495084	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs8032762	1.00[YRI][hapmap]
rs8039418	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs8043494	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs983067	0.84[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
rs11072411	TBC1D21	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73520600-73579600	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:73527000-73579400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:73535200-73588000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:73536200-73602000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:73538000-73593400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:73540000-73584800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:73544400-73583000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:73546800-73583000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:73546800-73588600	Weak transcription	Spleen	Spleen
10	chr15:73547800-73584600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:73550800-73581400	Weak transcription	HMEC	breast
12	chr15:73552400-73588200	Weak transcription	Hela-S3	cervix
13	chr15:73552800-73598400	Weak transcription	Small Intestine	intestine
14	chr15:73553800-73581200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr15:73560800-73597200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr15:73562800-73583000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:73563200-73578800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:73563200-73598600	Weak transcription	Stomach Mucosa	stomach
19	chr15:73563400-73581000	Weak transcription	Fetal Brain Male	brain
20	chr15:73563400-73581200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:73563400-73585600	Strong transcription	Fetal Intestine Large	intestine
22	chr15:73563600-73578800	Weak transcription	A549	lung
23	chr15:73563600-73593600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:73566400-73597800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:73568600-73600800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr15:73570200-73597000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:73570400-73597000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:73571200-73601400	Strong transcription	Fetal Stomach	stomach
29	chr15:73572400-73587600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:73574000-73583600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:73574000-73596800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr15:73574400-73580000	Strong transcription	Brain Angular Gyrus	brain
33	chr15:73574600-73581200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:73574800-73588000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:73575000-73580200	Strong transcription	Fetal Intestine Small	intestine
36	chr15:73575000-73583600	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr15:73575000-73584200	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr15:73575200-73583600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:73575200-73583800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:73575600-73585600	Weak transcription	HepG2	liver
41	chr15:73576000-73578800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:73576000-73581000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:73576000-73586400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr15:73576200-73578600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:73576200-73580600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:73576200-73583000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:73576200-73585600	Weak transcription	Esophagus	oesophagus
48	chr15:73576200-73587600	Weak transcription	Right Ventricle	heart
49	chr15:73576400-73578600	Weak transcription	Left Ventricle	heart
50	chr15:73576400-73579000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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