Variant report

Variant	rs11637572
Chromosome Location	chr15:43685140-43685141
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr15:43685082-43685157	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
TUBGCP4	TF binding region
RN7SL487P	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1058298	0.91[EUR][1000 genomes]
rs1060939	0.80[AFR][1000 genomes]
rs1079309	0.84[CEU][hapmap];0.95[AFR][1000 genomes]
rs1095386	0.86[CHB][hapmap]
rs11070399	0.82[EUR][1000 genomes]
rs1133395	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12323999	0.85[ASN][1000 genomes]
rs12324584	0.85[ASN][1000 genomes]
rs12905772	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[EUR][1000 genomes]
rs1549525	0.86[CHB][hapmap]
rs1837959	0.87[CHB][hapmap]
rs1837960	0.86[CHB][hapmap]
rs1869258	0.81[AFR][1000 genomes]
rs2012467	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2243434	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs2244746	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[EUR][1000 genomes]
rs2244981	0.84[CEU][hapmap];0.95[AFR][1000 genomes]
rs2249952	0.83[EUR][1000 genomes]
rs2253268	0.84[CEU][hapmap];0.81[AFR][1000 genomes]
rs2264050	0.95[AFR][1000 genomes]
rs2278856	0.85[AFR][1000 genomes]
rs2278857	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs2278859	0.87[CHB][hapmap]
rs2278860	0.86[CHB][hapmap]
rs2412779	0.86[CHB][hapmap]
rs2412780	0.86[CHB][hapmap]
rs2412781	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2412782	0.83[ASN][1000 genomes]
rs2439845	0.83[EUR][1000 genomes]
rs2444036	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs2444037	0.94[EUR][1000 genomes]
rs2444251	0.84[CEU][hapmap]
rs2467733	0.82[ASN][1000 genomes]
rs2467737	0.83[EUR][1000 genomes]
rs2467738	0.81[CEU][hapmap]
rs2467745	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs2584700	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2584701	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2584702	0.85[ASN][1000 genomes]
rs2584703	0.87[ASN][1000 genomes]
rs2602141	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs28653441	0.83[ASN][1000 genomes]
rs28729853	0.81[ASN][1000 genomes]
rs2899082	0.86[CHB][hapmap]
rs2924369	0.95[AFR][1000 genomes]
rs3213990	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs3213991	0.82[ASN][1000 genomes]
rs3742969	0.86[CHB][hapmap]
rs3742971	0.91[CHB][hapmap]
rs3809482	0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4075674	0.86[CHB][hapmap]
rs4296223	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs4401024	0.82[EUR][1000 genomes]
rs4547312	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs478028	0.91[CHB][hapmap]
rs484029	0.86[CHB][hapmap]
rs488756	0.86[CHB][hapmap]
rs493377	0.84[CEU][hapmap]
rs507178	0.87[CHB][hapmap]
rs509306	0.84[EUR][1000 genomes]
rs529611	0.85[AFR][1000 genomes]
rs536313	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs542898	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs548704	0.95[AFR][1000 genomes]
rs560191	0.95[AFR][1000 genomes]
rs573615	0.86[CHB][hapmap]
rs6493083	0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6493084	0.82[EUR][1000 genomes]
rs6493085	0.86[CHB][hapmap]
rs6493086	0.81[EUR][1000 genomes]
rs6493087	0.87[CHB][hapmap]
rs6493088	0.82[ASN][1000 genomes]
rs689693	0.83[EUR][1000 genomes]
rs689767	0.82[CEU][hapmap];0.95[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs690012	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs690276	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs690367	0.84[CEU][hapmap];0.90[AFR][1000 genomes]
rs690446	0.85[AFR][1000 genomes]
rs690472	0.85[AFR][1000 genomes]
rs690512	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs693510	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs694725	0.84[CEU][hapmap]
rs7163245	0.81[ASN][1000 genomes]
rs7163288	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs7166812	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7167882	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7170152	0.82[EUR][1000 genomes]
rs7170489	0.87[CHB][hapmap]
rs7172374	0.82[EUR][1000 genomes]
rs7176849	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs8039638	0.91[CHB][hapmap]
rs8042688	0.82[EUR][1000 genomes]
rs884704	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs9920879	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs999026	0.82[ASN][1000 genomes]
rs999047	0.86[CHB][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats 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	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11637572	ZSCAN29	cis	multi-tissue	Pritchard
rs11637572	ZSCAN29	cis	Thyroid	GTEx
rs11637572	TGM5	cis	multi-tissue	Pritchard
rs11637572	TGM7	cis	Esophagus Mucosa	GTEx
rs11637572	AC011330.5	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43664000-43692600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:43664600-43687800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:43664600-43688000	Weak transcription	Stomach Mucosa	stomach
4	chr15:43664600-43695600	Weak transcription	Fetal Heart	heart
5	chr15:43665000-43687800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:43665000-43730000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:43665200-43686600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:43668000-43717800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:43668200-43702200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:43668200-43732800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:43670600-43703200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:43671400-43686600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:43675600-43744400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:43675800-43687000	Weak transcription	NHDF-Ad	bronchial
15	chr15:43676800-43695600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:43677400-43686000	Weak transcription	Fetal Lung	lung
17	chr15:43678000-43687000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:43678200-43686800	Weak transcription	A549	lung
19	chr15:43678200-43686800	Weak transcription	Osteobl	bone
20	chr15:43678200-43688800	Weak transcription	Fetal Brain Male	brain
21	chr15:43678400-43686400	Weak transcription	Gastric	stomach
22	chr15:43678400-43687200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:43678400-43688000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr15:43678400-43689200	Weak transcription	HUVEC	blood vessel
25	chr15:43678400-43693800	Weak transcription	Small Intestine	intestine
26	chr15:43678600-43686000	Weak transcription	Fetal Kidney	kidney
27	chr15:43678600-43686400	Weak transcription	Pancreas	Pancrea
28	chr15:43678600-43686800	Weak transcription	NHEK	skin
29	chr15:43678600-43687200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:43678600-43687800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr15:43678800-43686800	Weak transcription	Colonic Mucosa	Colon
32	chr15:43679200-43686800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:43679600-43686600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:43679600-43686800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:43679600-43686800	Weak transcription	HSMMtube	muscle
36	chr15:43679600-43686800	Weak transcription	NH-A	brain
37	chr15:43679600-43687000	Weak transcription	Brain Angular Gyrus	brain
38	chr15:43679600-43687000	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:43679600-43687600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr15:43679600-43687800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr15:43679600-43688000	Weak transcription	HSMM	muscle
42	chr15:43679800-43686800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr15:43679800-43686800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr15:43679800-43686800	Weak transcription	GM12878-XiMat	blood
45	chr15:43680200-43686800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:43680200-43686800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:43680200-43687800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:43680400-43686600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:43680400-43686800	Weak transcription	Aorta	Aorta
50	chr15:43680400-43686800	Weak transcription	Right Ventricle	heart

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