Variant report

Variant	rs6581155
Chromosome Location	chr12:58178162-58178163
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 36 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1021469	0.92[CEU][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10431505	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10431552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747786	0.83[JPT][hapmap]
rs10747787	0.83[JPT][hapmap]
rs10783847	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877011	0.85[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs10877012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877013	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877017	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877018	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877029	0.83[JPT][hapmap]
rs10877030	0.83[JPT][hapmap]
rs11172333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172342	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172344	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172349	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172350	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172367	0.83[JPT][hapmap]
rs11172369	0.83[JPT][hapmap]
rs1599931	0.88[JPT][hapmap]
rs1599932	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1875124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1875125	0.88[JPT][hapmap]
rs2014886	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2069502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2069506	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291617	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782130	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3825079	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4237844	0.83[JPT][hapmap]
rs4646536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760171	0.83[JPT][hapmap]
rs4760172	0.83[JPT][hapmap]
rs4760332	0.88[JPT][hapmap]
rs4760333	0.82[AFR][1000 genomes]
rs4760339	0.82[JPT][hapmap]
rs4760341	0.82[JPT][hapmap]
rs56177740	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs701008	0.81[TSI][hapmap]
rs703842	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs724834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7312623	0.83[JPT][hapmap]
rs7489290	0.82[YRI][hapmap]
rs7965287	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8181644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs870392	0.88[JPT][hapmap]
rs871871	0.88[JPT][hapmap]
rs923829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9652011	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:36)

SNP	Gene	Cis/trans	Tissue	Source
rs6581155	TSFM	cis	lymphoblastoid	seeQTL
rs6581155	METTL21B	cis	Nerve Tibial	GTEx
rs6581155	DKFZP586D0919	cis	multi-tissue	Pritchard
rs6581155	FAM119B	cis	Cerebellum	GTEx
rs6581155	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs6581155	TSFM	cis	cerebellum	SCAN
rs6581155	FAM119B	cis	Brain Pons	GTEx
rs6581155	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs6581155	METTL21B	cis	Adipose Subcutaneous	GTEx
rs6581155	GPR84	cis	cerebellum	SCAN
rs6581155	TSFM	cis	multi-tissue	Pritchard
rs6581155	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs6581155	XRCC6BP1	cis	Whole Blood	GTEx
rs6581155	TSPAN31	cis	cerebellum	SCAN
rs6581155	FAM119B	cis	parietal	SCAN
rs6581155	FAM119B	cis	Lymphoblastoid	GTEx
rs6581155	WIBG	cis	cerebellum	SCAN
rs6581155	METTL21B	cis	lung	GTEx
rs6581155	TSFM	cis	Muscle Skeletal	GTEx
rs6581155	KRT5	cis	cerebellum	SCAN
rs6581155	TSFM	cis	parietal	SCAN
rs6581155	FAM119B	cis	Frontal Cortex	GTEx
rs6581155	METTL21B	cis	Heart Left Ventricle	GTEx
rs6581155	TSPAN31	cis	parietal	SCAN
rs6581155	CDK4	cis	cerebellum	SCAN
rs6581155	METTL21B	cis	Esophagus Muscularis	GTEx
rs6581155	HSD17B6	cis	cerebellum	SCAN
rs6581155	METTL21B	cis	Muscle Skeletal	GTEx
rs6581155	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs6581155	KIAA0748	cis	cerebellum	SCAN
rs6581155	FAM119B	cis	cerebellum	SCAN
rs6581155	METTL21B	cis	Esophagus Mucosa	GTEx
rs6581155	ESPL1	cis	parietal	SCAN
rs6581155	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs6581155	METTL21B	cis	Whole Blood	GTEx
rs6581155	FAM119B	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58176600-58178200	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr12:58177200-58178200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:58177200-58179000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:58177200-58179000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:58177200-58179800	Weak transcription	Aorta	Aorta
6	chr12:58177200-58189800	Weak transcription	Small Intestine	intestine
7	chr12:58177200-58197200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:58177400-58178200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:58177400-58178200	Enhancers	Primary B cells from cord blood	blood
10	chr12:58177400-58178200	Enhancers	Primary T cells from cord blood	blood
11	chr12:58177400-58178200	Enhancers	Primary hematopoietic stem cells	blood
12	chr12:58177400-58178200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:58177400-58178200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr12:58177400-58178200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:58177400-58178200	Enhancers	Adipose Nuclei	Adipose
16	chr12:58177400-58178200	Enhancers	Brain Angular Gyrus	brain
17	chr12:58177400-58178200	Enhancers	HUVEC	blood vessel
18	chr12:58177400-58178400	Weak transcription	Fetal Stomach	stomach
19	chr12:58177400-58179000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:58177400-58179000	Weak transcription	Left Ventricle	heart
21	chr12:58177400-58179000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr12:58177400-58179000	Weak transcription	NH-A	brain
23	chr12:58177400-58179200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:58177400-58179200	Weak transcription	HSMMtube	muscle
25	chr12:58177400-58180000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:58177400-58180000	Weak transcription	Colonic Mucosa	Colon
27	chr12:58177400-58180000	Weak transcription	Ovary	ovary
28	chr12:58177400-58180000	Weak transcription	Psoas Muscle	Psoas
29	chr12:58177400-58180000	Weak transcription	Spleen	Spleen
30	chr12:58177400-58180200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:58177400-58180200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr12:58177400-58190000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr12:58177400-58192800	Weak transcription	Stomach Mucosa	stomach
34	chr12:58177400-58200400	Weak transcription	Fetal Heart	heart
35	chr12:58177400-58216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:58177600-58178200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr12:58177600-58178200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr12:58177600-58178200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr12:58177600-58178200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:58177600-58178200	Genic enhancers	Brain Substantia Nigra	brain
41	chr12:58177600-58178200	Genic enhancers	Duodenum Mucosa	Duodenum
42	chr12:58177600-58178200	Enhancers	Fetal Brain Female	brain
43	chr12:58177600-58178200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
44	chr12:58177600-58178200	Flanking Active TSS	GM12878-XiMat	blood
45	chr12:58177600-58178200	Enhancers	HMEC	breast
46	chr12:58177600-58178200	Genic enhancers	NHEK	skin
47	chr12:58177600-58179000	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr12:58177600-58179000	Weak transcription	Brain Anterior Caudate	brain
49	chr12:58177600-58179000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr12:58177600-58179200	Weak transcription	H1 Cell Line	embryonic stem cell

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