Variant report

Variant	rs492562
Chromosome Location	chr6:118906223-118906224
allele	G/T
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	SETDB1	chr6:118906178-118906445	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:118905497..118907408-chr6:118920434..118922584,2	MCF-7	breast:
2	chr6:118904992..118906769-chr6:118911798..118913506,2	MCF-7	breast:

Variant related genes	Relation type
SSXP10	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1016095	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10457344	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10484287	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1051429	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11153758	0.84[ASN][1000 genomes]
rs11153761	0.85[CHB][hapmap]
rs12153938	0.83[ASN][1000 genomes]
rs12204456	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs12526557	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12530169	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1547326	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs17080423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1936059	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2181513	0.81[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2187945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2356178	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2356184	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2356502	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs25421	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs25423	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs3734382	0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4027728	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs422312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4502975	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs482910	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs485416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946343	0.87[ASN][1000 genomes]
rs4946348	0.84[ASN][1000 genomes]
rs4946349	0.81[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs516212	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516463	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541442	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6569021	0.83[ASN][1000 genomes]
rs6569022	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6569023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6911599	0.85[YRI][hapmap]
rs6919887	0.81[CHB][hapmap]
rs6928336	0.84[ASN][1000 genomes]
rs6929390	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs763255	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7740922	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs7741644	0.86[JPT][hapmap]
rs7742696	0.87[ASN][1000 genomes]
rs7749208	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7749694	0.85[JPT][hapmap]
rs7751213	0.84[ASN][1000 genomes]
rs7754293	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7757337	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7757407	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7759088	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7762990	0.84[CHB][hapmap]
rs7763904	0.84[ASN][1000 genomes]
rs933257	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9372506	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9374733	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9374735	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9374736	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9387586	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9387596	0.85[CEU][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs9401073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9401081	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9481815	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9481819	0.86[JPT][hapmap]
rs9481832	0.84[ASN][1000 genomes]
rs9481840	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9489403	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs9489414	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9489419	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9489420	0.86[JPT][hapmap]
rs9489424	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs9489432	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9489437	0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs9489438	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9489439	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9489446	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs9489448	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9489449	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs9489454	0.84[ASN][1000 genomes]
rs9489455	0.84[ASN][1000 genomes]
rs9489456	0.81[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9489461	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9489478	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs9689896	0.81[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1025456	chr6:118669672-119058789	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS 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	10 gene(s)	inside rSNPs	diseases
8	nsv432958	chr6:118692307-119010307	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv1034448	chr6:118698169-119016383	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1025097	chr6:118699752-119058789	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
11	nsv532052	chr6:118711850-119057295	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv432959	chr6:118716318-119010307	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv604556	chr6:118722589-119065365	Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
14	nsv949416	chr6:118772508-119033063	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv948980	chr6:118772508-119137658	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	nsv604559	chr6:118786486-119113317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv1022865	chr6:118786586-119058789	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
18	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	nsv1030331	chr6:118874345-118975680	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
20	nsv969439	chr6:118900716-118913670	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs492562	SSXP10	cis	Artery Tibial	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118895800-118911400	Weak transcription	Right Ventricle	heart
2	chr6:118896000-118909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:118896200-118910000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:118900400-118910200	Weak transcription	Fetal Lung	lung
5	chr6:118900400-118911200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:118901000-118926200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:118901400-118908000	Enhancers	Psoas Muscle	Psoas
8	chr6:118901400-118913000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:118901600-118906400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:118901600-118912000	Strong transcription	Primary T cells from cord blood	blood
11	chr6:118902000-118927400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:118902200-118910400	Weak transcription	Ovary	ovary
13	chr6:118902200-118911400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:118902200-118911600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:118902200-118939800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:118902400-118908200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:118902400-118917400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:118902400-118918000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:118902400-118924800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:118902400-118927400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:118902600-118909800	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:118902800-118911200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:118902800-118911200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:118903000-118906600	Strong transcription	Fetal Thymus	thymus
25	chr6:118903000-118910000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:118903200-118907000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr6:118903200-118910800	Weak transcription	NHLF	lung
28	chr6:118903400-118907000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:118903600-118907600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:118903600-118924200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:118903800-118907600	Weak transcription	Pancreas	Pancrea
32	chr6:118903800-118910600	Weak transcription	Osteobl	bone
33	chr6:118903800-118911400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:118904000-118924200	Weak transcription	Primary B cells from cord blood	blood
35	chr6:118904400-118907600	Weak transcription	Stomach Mucosa	stomach
36	chr6:118904400-118908000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr6:118904400-118911200	Weak transcription	Thymus	Thymus
38	chr6:118904400-118916200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr6:118904400-118926200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:118904400-118930000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr6:118904600-118908200	Weak transcription	Gastric	stomach
42	chr6:118905000-118907400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr6:118905000-118909800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:118905600-118907200	Strong transcription	Dnd41	blood
45	chr6:118905600-118907400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr6:118905800-118906400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:118905800-118906400	Enhancers	Right Atrium	heart
48	chr6:118906000-118906800	Strong transcription	Fetal Muscle Leg	muscle
49	chr6:118906000-118907200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr6:118906200-118906400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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