Variant report

Variant	rs675090
Chromosome Location	chr11:64700767-64700768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64697755..64701101-chr11:64701651..64703886,3	MCF-7	breast:
2	chr11:64645778..64647784-chr11:64698731..64701222,2	K562	blood:
3	chr11:64689194..64695395-chr11:64699461..64704301,10	K562	blood:
4	chr11:64700459..64702214-chr11:64704518..64706728,2	K562	blood:
5	chr11:64621756..64624358-chr11:64698896..64701466,2	K562	blood:

Variant related genes	Relation type
ENSG00000110047	Chromatin interaction
ENSG00000068971	Chromatin interaction
ENSG00000149735	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11231913	0.83[ASN][1000 genomes]
rs17146441	0.84[TSI][hapmap]
rs2285346	0.84[CEU][hapmap];0.86[CHB][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap]
rs240565	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2518909	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2670908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35131180	0.86[EUR][1000 genomes]
rs470511	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs519796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs574381	0.87[CHB][hapmap]
rs594392	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs610130	0.89[ASN][1000 genomes]
rs618006	0.87[CHB][hapmap]
rs626670	0.83[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs67301043	0.85[EUR][1000 genomes]
rs673995	0.81[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.92[MKK][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs688749	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
2	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
3	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
4	nsv897704	chr11:64584987-64701030	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
5	nsv897705	chr11:64591679-64701030	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
6	nsv897706	chr11:64591679-64721908	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
7	nsv897707	chr11:64600002-64701030	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
8	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
9	nsv555208	chr11:64645119-64771179	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1029 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs675090	SPDYC	cis	Whole Blood	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64692800-64702200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:64693000-64702000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr11:64693000-64702600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr11:64693000-64703000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:64693000-64703000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:64693000-64703000	Weak transcription	Fetal Kidney	kidney
7	chr11:64693000-64703000	Weak transcription	K562	blood
8	chr11:64693000-64703600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:64693200-64701400	Weak transcription	Fetal Heart	heart
10	chr11:64693200-64702800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:64693200-64702800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:64693600-64701400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:64693600-64703000	Weak transcription	Stomach Mucosa	stomach
14	chr11:64693800-64700800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:64693800-64700800	Weak transcription	HepG2	liver
16	chr11:64693800-64704400	Weak transcription	Right Atrium	heart
17	chr11:64694000-64701000	Strong transcription	Fetal Intestine Small	intestine
18	chr11:64694000-64702200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:64694000-64702600	Strong transcription	Fetal Muscle Leg	muscle
20	chr11:64694000-64702800	Strong transcription	Fetal Brain Female	brain
21	chr11:64694000-64702800	Strong transcription	Fetal Stomach	stomach
22	chr11:64694000-64702800	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:64694000-64703000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:64694000-64703000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:64694200-64700800	Strong transcription	Fetal Intestine Large	intestine
26	chr11:64694200-64701600	Strong transcription	Colon Smooth Muscle	Colon
27	chr11:64694200-64701800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr11:64694200-64702000	Strong transcription	Aorta	Aorta
29	chr11:64694200-64702000	Strong transcription	Left Ventricle	heart
30	chr11:64694200-64702200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:64694200-64702400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:64694200-64702400	Strong transcription	Gastric	stomach
33	chr11:64694200-64703000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:64694200-64703000	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr11:64694200-64703000	Strong transcription	Colonic Mucosa	Colon
36	chr11:64694200-64703000	Weak transcription	GM12878-XiMat	blood
37	chr11:64694200-64703200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:64694200-64703200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:64694400-64701400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr11:64694400-64701400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:64694400-64701600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:64694400-64702400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:64694400-64702600	Weak transcription	Fetal Brain Male	brain
44	chr11:64694400-64702600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr11:64694400-64702600	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr11:64694400-64702800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:64694400-64702800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr11:64694400-64702800	Strong transcription	Brain Germinal Matrix	brain
49	chr11:64694400-64702800	Strong transcription	Esophagus	oesophagus
50	chr11:64694400-64702800	Strong transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links