Variant report

Variant	rs1006586
Chromosome Location	chr11:86226645-86226646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:86219227..86220882-chr11:86224339..86227015,2	K562	blood:
2	chr11:86224834..86227420-chr11:86229553..86231855,2	K562	blood:
3	chr11:86209598..86213474-chr11:86222640..86227259,4	K562	blood:
4	chr11:86224152..86227397-chr11:86232854..86235365,3	MCF-7	breast:
5	chr11:86221104..86225436-chr11:86225475..86228538,5	K562	blood:
6	chr11:86225920..86228246-chr11:86229553..86231799,2	K562	blood:
7	chr11:86221142..86225436-chr11:86225475..86228641,4	K562	blood:
8	chr11:86226207..86227795-chr11:86510451..86512542,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1006587	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444371	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs10444372	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs10444373	1.00[ASN][1000 genomes]
rs10501622	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs10898488	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10898495	1.00[ASN][1000 genomes]
rs11234643	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs11234668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12361416	0.94[ASN][1000 genomes]
rs12362900	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12420965	1.00[CHB][hapmap]
rs12421147	1.00[ASN][1000 genomes]
rs12791972	0.83[ASN][1000 genomes]
rs12792300	0.94[ASN][1000 genomes]
rs12793707	1.00[ASN][1000 genomes]
rs12799562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs12808738	0.83[ASN][1000 genomes]
rs17149169	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28895937	1.00[ASN][1000 genomes]
rs34405620	1.00[ASN][1000 genomes]
rs35042210	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3758877	1.00[CHB][hapmap]
rs3758878	1.00[CHB][hapmap]
rs3824952	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs628449	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs7112309	1.00[CHB][hapmap]
rs72953626	1.00[ASN][1000 genomes]
rs7926965	1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7944836	0.85[ASW][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9645703	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv898056	chr11:86156848-86304402	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1006586	PCF11	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86172400-86227000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr11:86211600-86229800	Weak transcription	Brain Anterior Caudate	brain
3	chr11:86215000-86229800	Weak transcription	Lung	lung
4	chr11:86215800-86230000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:86218000-86228000	Weak transcription	Fetal Brain Female	brain
6	chr11:86218200-86227800	Weak transcription	Fetal Brain Male	brain
7	chr11:86218600-86227800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr11:86218600-86229600	Weak transcription	Brain Germinal Matrix	brain
9	chr11:86220000-86230600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr11:86222400-86227000	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr11:86222800-86227000	Weak transcription	Ovary	ovary
12	chr11:86222800-86227200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr11:86223000-86229800	Weak transcription	Gastric	stomach
14	chr11:86223000-86238200	Weak transcription	Pancreas	Pancrea
15	chr11:86223200-86230600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:86223800-86236800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr11:86223800-86237000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:86224000-86227400	Enhancers	Placenta Amnion	Placenta Amnion
19	chr11:86224600-86229200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:86224600-86230000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:86224600-86230000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:86224800-86226800	Weak transcription	Fetal Intestine Small	intestine
23	chr11:86224800-86229600	Weak transcription	Small Intestine	intestine
24	chr11:86224800-86232400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:86225000-86228600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:86225000-86230200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:86225400-86231000	Enhancers	NHEK	skin
28	chr11:86225400-86233200	Enhancers	HUVEC	blood vessel
29	chr11:86225600-86228200	Weak transcription	Psoas Muscle	Psoas
30	chr11:86225600-86230800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:86225800-86227200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:86225800-86227400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr11:86225800-86231400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:86226000-86226800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr11:86226200-86226800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:86226200-86227000	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr11:86226200-86229200	Weak transcription	Fetal Kidney	kidney
38	chr11:86226200-86229200	Enhancers	HMEC	breast
39	chr11:86226200-86231600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:86226400-86226800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:86226400-86227000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr11:86226400-86227000	Enhancers	Placenta	Placenta
43	chr11:86226400-86227000	Enhancers	Fetal Stomach	stomach
44	chr11:86226400-86227000	Enhancers	Spleen	Spleen
45	chr11:86226400-86227200	Enhancers	Fetal Lung	lung
46	chr11:86226400-86227200	Enhancers	Right Ventricle	heart
47	chr11:86226400-86227400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:86226400-86227400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr11:86226400-86227400	Enhancers	HSMM	muscle
50	chr11:86226400-86227400	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links