Variant report

Variant	rs953871
Chromosome Location	chr11:33791981-33791982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10836108	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1096558	0.85[ASN][1000 genomes]
rs1096559	0.85[ASN][1000 genomes]
rs1096563	0.85[ASN][1000 genomes]
rs11032363	0.96[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs11032366	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11032374	0.89[EUR][1000 genomes]
rs11032380	0.87[CEU][hapmap];0.83[TSI][hapmap]
rs1112840	0.89[EUR][1000 genomes]
rs12146621	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12282096	0.87[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes]
rs12361553	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs1402953	0.96[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs1402957	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1464484	0.86[AMR][1000 genomes]
rs1464486	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464487	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522087	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1578986	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1738547	0.85[ASN][1000 genomes]
rs1738548	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs2056396	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs2140066	0.85[AMR][1000 genomes]
rs2272065	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2901376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3181274	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs34944910	0.89[EUR][1000 genomes]
rs35162575	0.89[EUR][1000 genomes]
rs4755340	0.82[CEU][hapmap]
rs4756025	0.82[CEU][hapmap]
rs704702	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs704703	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7125621	0.87[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs7927218	0.87[CEU][hapmap];0.85[AMR][1000 genomes]
rs831594	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831596	0.91[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831603	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs939804	0.83[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523356	chr11:33777334-33797408	Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs953871	CD59	Cis_1M	lymphoblastoid	RTeQTL
rs953871	APIP	cis	cerebellum	SCAN
rs953871	FBXO3	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:33758800-33795000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:33759000-33795200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:33763200-33792200	Strong transcription	Fetal Thymus	thymus
4	chr11:33763200-33792400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:33764200-33792000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:33764400-33792200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr11:33764400-33792400	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr11:33764400-33792400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:33765400-33793800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:33767600-33792400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr11:33767800-33792200	Strong transcription	Adipose Nuclei	Adipose
12	chr11:33767800-33792400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr11:33769600-33795000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:33776800-33792200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:33777000-33792200	Strong transcription	Fetal Lung	lung
16	chr11:33777200-33792400	Strong transcription	Primary B cells from cord blood	blood
17	chr11:33778200-33792200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:33778800-33794600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:33779600-33795000	Weak transcription	Colonic Mucosa	Colon
20	chr11:33780000-33792200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr11:33782200-33792000	Weak transcription	Aorta	Aorta
22	chr11:33782200-33793400	Weak transcription	Right Ventricle	heart
23	chr11:33783800-33792000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr11:33784600-33792000	Strong transcription	Fetal Intestine Large	intestine
25	chr11:33784600-33792200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:33784600-33792200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr11:33784600-33792200	Strong transcription	Dnd41	blood
28	chr11:33784800-33792200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr11:33785000-33792400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr11:33785200-33792400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:33785200-33792400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr11:33785400-33792400	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr11:33785800-33792000	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr11:33786200-33792400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:33786200-33793200	Weak transcription	K562	blood
36	chr11:33786200-33793400	Weak transcription	A549	lung
37	chr11:33786200-33793600	Weak transcription	Fetal Heart	heart
38	chr11:33786200-33793600	Weak transcription	Small Intestine	intestine
39	chr11:33786400-33792200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:33786600-33792200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr11:33786600-33794000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr11:33787000-33792400	Strong transcription	Brain Cingulate Gyrus	brain
43	chr11:33787200-33792000	Strong transcription	Brain Substantia Nigra	brain
44	chr11:33787600-33794400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr11:33787600-33795000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr11:33787800-33794000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr11:33787800-33794200	Weak transcription	Fetal Intestine Small	intestine
48	chr11:33788000-33792400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr11:33788000-33793600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:33788000-33794000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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