Variant report

Variant	rs523156
Chromosome Location	chr15:43811843-43811844
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	15:43807815-43812531..15:44001645-44015047	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000238494	Chromatin interaction
ENSG00000242866	Chromatin interaction
ENSG00000166763	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1060939	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1079309	0.87[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12905772	0.87[CEU][hapmap]
rs1814538	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs1869258	0.96[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2242069	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs2244981	0.87[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2245715	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2249952	0.84[AMR][1000 genomes]
rs2251844	0.95[ASN][1000 genomes]
rs2253268	0.87[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2253708	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2254927	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255042	0.97[ASN][1000 genomes]
rs2255051	0.92[ASN][1000 genomes]
rs2255410	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255440	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2255663	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2264050	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2264876	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs2278857	0.83[CEU][hapmap];0.87[MEX][hapmap]
rs2412781	0.87[CEU][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap]
rs2439831	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2439832	0.95[JPT][hapmap]
rs2439834	0.87[ASN][1000 genomes]
rs2439839	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2439843	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2439845	0.85[AMR][1000 genomes]
rs2439846	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2439850	0.95[JPT][hapmap]
rs2444032	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2444244	0.92[ASN][1000 genomes]
rs2444250	0.95[JPT][hapmap]
rs2444251	0.87[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2467736	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2467737	0.85[AMR][1000 genomes]
rs2467738	0.91[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2467739	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2467741	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2467742	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2467745	0.87[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs2470130	0.97[ASN][1000 genomes]
rs2470131	0.97[ASN][1000 genomes]
rs2584725	0.81[ASN][1000 genomes]
rs2602141	0.87[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs28649346	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2915788	0.92[ASN][1000 genomes]
rs2924369	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2927070	0.80[AMR][1000 genomes]
rs2927071	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs3097773	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3809482	0.87[CEU][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap]
rs4296223	0.87[CEU][hapmap];0.91[MEX][hapmap]
rs4547312	0.83[CEU][hapmap];0.87[MEX][hapmap]
rs475486	0.90[ASN][1000 genomes]
rs480108	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs486301	0.95[ASN][1000 genomes]
rs493377	0.87[CEU][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs495175	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs496584	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs506120	0.87[CEU][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs518288	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs529611	0.96[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs536313	0.87[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs537115	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs542898	0.84[AMR][1000 genomes]
rs548704	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs560191	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs570933	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs572837	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573615	0.87[MEX][hapmap];0.88[MKK][hapmap]
rs6493083	0.87[CEU][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap]
rs689647	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs689693	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs689767	0.87[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes]
rs689781	0.81[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs689797	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689826	0.95[JPT][hapmap]
rs689835	0.95[JPT][hapmap]
rs689883	0.99[ASN][1000 genomes]
rs690012	0.84[AMR][1000 genomes]
rs690276	0.87[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs690316	0.91[JPT][hapmap]
rs690367	0.87[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs690436	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs690446	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs690466	0.95[JPT][hapmap]
rs690472	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs690512	0.87[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs693510	0.87[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs694725	0.87[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs694985	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7163288	0.87[CEU][hapmap];0.91[MEX][hapmap]
rs7497780	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920879	0.87[CEU][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
3	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv437799	chr15:43784000-43989518	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv515877	chr15:43802024-43818052	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv518707	chr15:43802024-43826557	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv832988	chr15:43804641-43976862	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs523156	STRC	cis	multi-tissue	Pritchard
rs523156	ZNF690	cis	multi-tissue	Pritchard
rs523156	TGM5	cis	lymphoblastoid	seeQTL
rs523156	ZSCAN29	cis	multi-tissue	Pritchard
rs523156	AC011330.5	cis	Artery Tibial	GTEx
rs523156	TGM7	cis	Esophagus Mucosa	GTEx
rs523156	AC011330.5	cis	Thyroid	GTEx
rs523156	TGM5	cis	multi-tissue	Pritchard
rs523156	STRCP1	cis	Whole Blood	GTEx
rs523156	ZSCAN29	cis	Thyroid	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43808000-43812000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:43808400-43812000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:43809600-43812200	Active TSS	HSMMtube	muscle
4	chr15:43810400-43826200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:43810600-43826400	Weak transcription	Spleen	Spleen
6	chr15:43810800-43812000	Enhancers	Placenta	Placenta
7	chr15:43810800-43814200	Weak transcription	Gastric	stomach
8	chr15:43810800-43817600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:43810800-43824000	Weak transcription	Fetal Kidney	kidney
10	chr15:43810800-43826000	Weak transcription	Esophagus	oesophagus
11	chr15:43811000-43812000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:43811000-43812000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:43811000-43812000	Flanking Active TSS	Fetal Thymus	thymus
14	chr15:43811000-43812000	Flanking Active TSS	Dnd41	blood
15	chr15:43811000-43812600	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr15:43811000-43812600	Weak transcription	Left Ventricle	heart
17	chr15:43811000-43812800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:43811000-43812800	Weak transcription	Ovary	ovary
19	chr15:43811000-43814200	Weak transcription	Lung	lung
20	chr15:43811000-43818600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:43811000-43828600	Weak transcription	Pancreas	Pancrea
22	chr15:43811200-43812000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:43811200-43812000	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr15:43811200-43812000	Genic enhancers	Fetal Stomach	stomach
25	chr15:43811200-43812200	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr15:43811200-43812200	Weak transcription	Fetal Intestine Large	intestine
27	chr15:43811200-43812400	Weak transcription	Aorta	Aorta
28	chr15:43811200-43812600	Enhancers	Primary hematopoietic stem cells	blood
29	chr15:43811200-43812800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:43811200-43812800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr15:43811200-43813600	Weak transcription	Adipose Nuclei	Adipose
32	chr15:43811200-43813600	Weak transcription	Fetal Intestine Small	intestine
33	chr15:43811200-43813800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr15:43811200-43820600	Weak transcription	Colonic Mucosa	Colon
35	chr15:43811200-43823600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:43811200-43826800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:43811400-43812000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr15:43811400-43812000	Enhancers	Fetal Brain Male	brain
39	chr15:43811400-43812000	Flanking Active TSS	NHDF-Ad	bronchial
40	chr15:43811400-43812000	Transcr. at gene 5' and 3'	NHLF	lung
41	chr15:43811400-43812200	Genic enhancers	Fetal Muscle Leg	muscle
42	chr15:43811400-43812400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:43811400-43812600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:43811400-43812600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:43811400-43812600	Enhancers	K562	blood
46	chr15:43811400-43812800	Weak transcription	Primary T cells from cord blood	blood
47	chr15:43811400-43812800	Weak transcription	Fetal Lung	lung
48	chr15:43811400-43813000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr15:43811400-43829200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr15:43811600-43812000	Flanking Active TSS	Brain Substantia Nigra	brain

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