Variant report

Variant	rs2276443
Chromosome Location	chr11:75153031-75153032
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:75152364-75154108	K562	blood:	n/a	n/a
2	POLR2A	chr11:75152992-75153251	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:75109252..75112429-chr11:75150436..75153898,3	MCF-7	breast:
2	chr11:75110249..75114230-chr11:75150071..75153287,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL35-3	chr11:75152936-75153686	ucscGeneNc_uc001owz_2

No data

Variant related genes	Relation type
GDPD5	TF binding region
ENSG00000206941	Chromatin interaction
ENSG00000149273	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11236444	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[LWK][hapmap];0.84[EUR][1000 genomes]
rs11600640	0.90[CHB][hapmap]
rs12272513	0.91[AFR][1000 genomes]
rs12277708	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12289922	0.91[AFR][1000 genomes]
rs12292511	0.91[AFR][1000 genomes]
rs12292958	0.91[AFR][1000 genomes]
rs12421913	0.90[CHB][hapmap]
rs2187568	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3814715	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs55955041	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56010007	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56207324	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56386896	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56412430	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56851635	0.86[EUR][1000 genomes]
rs61897372	0.89[EUR][1000 genomes]
rs61897374	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61897376	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61897380	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61897406	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61897410	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61897411	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61897413	0.92[EUR][1000 genomes]
rs61897414	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61897415	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61897416	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61897419	0.84[EUR][1000 genomes]
rs7125082	0.89[CEU][hapmap];0.82[CHB][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs7128197	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7131225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73494872	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041640	chr11:74945824-75174688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
2	nsv897920	chr11:75087520-75181249	Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv897923	chr11:75129007-75302855	Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2276443	GDPD5	cis	multi-tissue	Pritchard
rs2276443	GDPD5	cis	lymphoblastoid	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75141800-75165400	Weak transcription	Right Atrium	heart
2	chr11:75142000-75165200	Weak transcription	Ovary	ovary
3	chr11:75142600-75156600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr11:75144200-75164800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:75144200-75165400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:75144200-75186600	Weak transcription	Gastric	stomach
7	chr11:75144400-75179800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:75144600-75155800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr11:75144600-75174000	Weak transcription	Liver	Liver
10	chr11:75144800-75156600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:75145000-75156000	Strong transcription	Spleen	Spleen
12	chr11:75145000-75162400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr11:75145000-75167800	Strong transcription	Placenta	Placenta
14	chr11:75145200-75165200	Weak transcription	A549	lung
15	chr11:75145200-75186200	Weak transcription	Primary T cells from cord blood	blood
16	chr11:75145200-75186400	Strong transcription	Fetal Intestine Small	intestine
17	chr11:75145400-75156200	Strong transcription	Fetal Intestine Large	intestine
18	chr11:75145600-75155400	Strong transcription	Adipose Nuclei	Adipose
19	chr11:75146400-75163200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr11:75146400-75173000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:75147800-75186000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr11:75148000-75163800	Weak transcription	Lung	lung
23	chr11:75148200-75186000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:75149400-75155600	Strong transcription	HSMMtube	muscle
25	chr11:75150400-75153400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:75150400-75172600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:75150800-75156600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:75151400-75154200	Weak transcription	Fetal Brain Female	brain
29	chr11:75151400-75158800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:75151800-75154400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr11:75152000-75153400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:75152000-75154000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:75152200-75153400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
34	chr11:75152200-75153400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:75152200-75153400	Enhancers	Esophagus	oesophagus
36	chr11:75152400-75153600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr11:75152600-75153800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr11:75152800-75153200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:75152800-75153400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
40	chr11:75152800-75153400	Bivalent Enhancer	NHEK	skin
41	chr11:75152800-75159400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr11:75152800-75161600	Weak transcription	Pancreas	Pancrea
43	chr11:75153000-75153800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr11:75153000-75161200	Weak transcription	Right Ventricle	heart
45	chr11:75153000-75162200	Weak transcription	HepG2	liver
46	chr11:75153000-75162800	Weak transcription	Primary T cells fromperipheralblood	blood

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