Variant report

Variant	rs673995
Chromosome Location	chr11:64702200-64702201
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64683512..64686373-chr11:64701129..64703249,2	MCF-7	breast:
2	chr11:64701027..64702913-chr11:64893913..64895958,2	K562	blood:
3	chr11:64681545..64685255-chr11:64700864..64703818,3	K562	blood:
4	chr11:64691374..64695669-chr11:64701131..64705582,6	MCF-7	breast:
5	chr11:64689194..64695395-chr11:64699461..64704301,10	K562	blood:
6	chr11:64700459..64702214-chr11:64704518..64706728,2	K562	blood:
7	chr11:64645500..64648132-chr11:64701780..64703587,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110047	Chromatin interaction
ENSG00000068971	Chromatin interaction
ENSG00000110046	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2285346	0.88[YRI][hapmap]
rs240567	0.87[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.94[MKK][hapmap];0.94[YRI][hapmap]
rs240571	0.87[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.94[MKK][hapmap];0.94[YRI][hapmap]
rs240572	0.87[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.94[MKK][hapmap];0.94[YRI][hapmap]
rs2670908	0.87[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.94[MKK][hapmap];0.88[YRI][hapmap]
rs470511	0.81[ASN][1000 genomes]
rs519796	0.87[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.94[MKK][hapmap];0.88[YRI][hapmap]
rs626670	0.86[MKK][hapmap]
rs675090	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]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
rs673995	SPDYC	cis	Whole Blood	GTEx

Chromatin state (count:121 , 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	chr11:64693000-64702600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr11:64693000-64703000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:64693000-64703000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr11:64693000-64703000	Weak transcription	Fetal Kidney	kidney
6	chr11:64693000-64703000	Weak transcription	K562	blood
7	chr11:64693000-64703600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr11:64693200-64702800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:64693200-64702800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:64693600-64703000	Weak transcription	Stomach Mucosa	stomach
11	chr11:64693800-64704400	Weak transcription	Right Atrium	heart
12	chr11:64694000-64702200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr11:64694000-64702600	Strong transcription	Fetal Muscle Leg	muscle
14	chr11:64694000-64702800	Strong transcription	Fetal Brain Female	brain
15	chr11:64694000-64702800	Strong transcription	Fetal Stomach	stomach
16	chr11:64694000-64702800	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:64694000-64703000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:64694000-64703000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:64694200-64702200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:64694200-64702400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr11:64694200-64702400	Strong transcription	Gastric	stomach
22	chr11:64694200-64703000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:64694200-64703000	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr11:64694200-64703000	Strong transcription	Colonic Mucosa	Colon
25	chr11:64694200-64703000	Weak transcription	GM12878-XiMat	blood
26	chr11:64694200-64703200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:64694200-64703200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:64694400-64702400	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:64694400-64702600	Weak transcription	Fetal Brain Male	brain
30	chr11:64694400-64702600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr11:64694400-64702600	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr11:64694400-64702800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:64694400-64702800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:64694400-64702800	Strong transcription	Brain Germinal Matrix	brain
35	chr11:64694400-64702800	Strong transcription	Esophagus	oesophagus
36	chr11:64694400-64702800	Strong transcription	Right Ventricle	heart
37	chr11:64694400-64702800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr11:64694400-64703000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:64694400-64703000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:64694400-64703000	Strong transcription	NHEK	skin
41	chr11:64694400-64703200	Strong transcription	Adipose Nuclei	Adipose
42	chr11:64694600-64703000	Strong transcription	Liver	Liver
43	chr11:64694600-64703200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:64694800-64702800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:64694800-64703600	Strong transcription	Spleen	Spleen
46	chr11:64695000-64702400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr11:64695200-64703400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr11:64695400-64702200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr11:64695400-64702200	Strong transcription	Rectal Smooth Muscle	rectum
50	chr11:64696000-64702400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links