Variant report

Variant	rs1465131
Chromosome Location	chr6:11192575-11192576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1885662	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2078599	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2146341	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2327338	0.86[MEX][hapmap]
rs4053067	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4711193	0.84[CEU][hapmap]
rs4711194	0.83[CEU][hapmap]
rs4713247	0.93[CEU][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs6456970	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7746976	0.84[CEU][hapmap]
rs7750787	0.86[MEX][hapmap]
rs9368610	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs941982	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1465131	SNRNP48	cis	cerebellum	SCAN
rs1465131	GCNT2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11172800-11195000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:11179000-11202200	Weak transcription	Brain Substantia Nigra	brain
3	chr6:11180200-11194600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:11180600-11194400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:11180800-11194800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:11181600-11196200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:11182000-11194000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:11182400-11194000	Strong transcription	NH-A	brain
9	chr6:11182400-11195200	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr6:11182600-11194800	Strong transcription	Primary B cells from cord blood	blood
11	chr6:11183000-11199000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr6:11183200-11195000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:11183400-11194000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:11183400-11194000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:11183400-11194000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:11183400-11194000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr6:11183400-11194600	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:11183400-11194600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:11183400-11195000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:11183600-11194200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:11183800-11194000	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:11184000-11192600	Strong transcription	Rectal Smooth Muscle	rectum
23	chr6:11184000-11194000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:11184000-11194000	Strong transcription	Primary T cells from cord blood	blood
25	chr6:11184000-11194000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:11184000-11194000	Strong transcription	Adipose Nuclei	Adipose
27	chr6:11184000-11194000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr6:11184000-11194000	Strong transcription	Thymus	Thymus
29	chr6:11184000-11194000	Strong transcription	HUVEC	blood vessel
30	chr6:11184000-11194200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:11184000-11194600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr6:11184200-11193800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:11184200-11194000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:11184400-11193000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:11184400-11195000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:11184400-11197000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:11184600-11194000	Strong transcription	Fetal Stomach	stomach
38	chr6:11185800-11193800	Strong transcription	Left Ventricle	heart
39	chr6:11185800-11193800	Weak transcription	Right Atrium	heart
40	chr6:11185800-11194000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:11185800-11194000	Strong transcription	Placenta	Placenta
42	chr6:11185800-11194400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:11185800-11202600	Weak transcription	Brain Angular Gyrus	brain
44	chr6:11186000-11194200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr6:11186000-11195000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:11186000-11195200	Weak transcription	Psoas Muscle	Psoas
47	chr6:11186800-11200400	Weak transcription	HMEC	breast
48	chr6:11187400-11194000	Strong transcription	HSMMtube	muscle
49	chr6:11187600-11194000	Strong transcription	Aorta	Aorta
50	chr6:11188400-11193600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links