Variant report

Variant	rs6496890
Chromosome Location	chr15:92619501-92619502
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:92611564..92613241-chr15:92617063..92619542,2	MCF-7	breast:
2	chr15:92397561..92399407-chr15:92617258..92620011,2	MCF-7	breast:
3	chr15:92613588..92616911-chr15:92617353..92620743,5	MCF-7	breast:
4	chr15:92395446..92397598-chr15:92618443..92620616,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176463	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11074038	0.86[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11074040	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1158683	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.84[ASN][1000 genomes]
rs12050741	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.80[ASN][1000 genomes]
rs12440470	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12591961	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12708590	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1400786	0.86[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs1543166	0.82[ASN][1000 genomes]
rs1543167	0.82[ASN][1000 genomes]
rs1568211	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2135853	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4247079	0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs4340310	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.84[ASN][1000 genomes]
rs4374150	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4499213	0.81[ASN][1000 genomes]
rs4530111	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4644836	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4984328	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4984329	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7167618	0.85[ASN][1000 genomes]
rs7168605	0.85[ASN][1000 genomes]
rs7171310	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177406	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181950	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030627	0.86[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs8041844	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs908650	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs908651	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs908655	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs992838	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.97[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	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1668	chr15:92585344-92635991	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6496890	MESP1	cis	cerebellum	SCAN
rs6496890	IDH2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92610800-92620400	Enhancers	Brain Substantia Nigra	brain
2	chr15:92613000-92620600	Weak transcription	Pancreas	Pancrea
3	chr15:92613400-92621000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:92613600-92620000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:92613600-92628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:92614200-92621000	Enhancers	Fetal Heart	heart
7	chr15:92614200-92621200	Enhancers	Brain Hippocampus Middle	brain
8	chr15:92614400-92621000	Enhancers	Lung	lung
9	chr15:92614600-92626600	Weak transcription	Psoas Muscle	Psoas
10	chr15:92615000-92634200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:92616200-92621000	Enhancers	Left Ventricle	heart
12	chr15:92616400-92619600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:92616400-92621000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:92616600-92620200	Enhancers	Primary hematopoietic stem cells	blood
15	chr15:92616600-92622800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr15:92616800-92619600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:92616800-92620800	Enhancers	Right Atrium	heart
18	chr15:92616800-92621600	Enhancers	Right Ventricle	heart
19	chr15:92617000-92621200	Enhancers	Brain Cingulate Gyrus	brain
20	chr15:92617400-92620200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:92617400-92621000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:92617400-92621000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr15:92617400-92621600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:92617600-92619600	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr15:92617600-92619800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr15:92617600-92620200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr15:92617600-92620600	Enhancers	Adipose Nuclei	Adipose
28	chr15:92617600-92620800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr15:92617600-92620800	Enhancers	Spleen	Spleen
30	chr15:92617800-92622800	Weak transcription	Brain Anterior Caudate	brain
31	chr15:92618000-92619800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr15:92618000-92620600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:92618000-92622000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr15:92618200-92620800	Enhancers	Esophagus	oesophagus
35	chr15:92618400-92619600	Weak transcription	Brain Angular Gyrus	brain
36	chr15:92618400-92620600	Weak transcription	Fetal Thymus	thymus
37	chr15:92618800-92619600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr15:92618800-92619600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:92618800-92625200	Weak transcription	Ovary	ovary
40	chr15:92619000-92619600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:92619000-92620800	Weak transcription	Liver	Liver
42	chr15:92619000-92625000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:92619200-92620800	Enhancers	Fetal Brain Female	brain
44	chr15:92619200-92621400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:92619200-92630400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:92619200-92638000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:92619400-92620000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr15:92619400-92620000	Enhancers	NHEK	skin
49	chr15:92619400-92621000	Enhancers	Fetal Brain Male	brain
50	chr15:92619400-92625200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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