Variant report

Variant	rs11586691
Chromosome Location	chr1:151771667-151771668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151771040..151773951-chr1:151782694..151784484,3	K562	blood:
2	chr1:151770881..151774367-chr1:151786518..151790478,5	MCF-7	breast:
3	chr1:151770963..151775334-chr1:151775936..151780512,5	MCF-7	breast:
4	chr1:151771155..151774343-chr1:151777363..151779853,3	MCF-7	breast:
5	chr1:151763150..151767122-chr1:151771180..151776437,5	K562	blood:

Variant related genes	Relation type
ENSG00000213171	Chromatin interaction
ENSG00000182134	Chromatin interaction
ENSG00000203288	Chromatin interaction
ENSG00000143365	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1054475	0.85[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1123855	0.85[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11806815	0.98[EUR][1000 genomes]
rs12748967	0.99[EUR][1000 genomes]
rs12756855	0.98[EUR][1000 genomes]
rs1623480	0.91[EUR][1000 genomes]
rs1781420	0.92[EUR][1000 genomes]
rs1781421	0.85[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs1781423	0.85[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs1781424	0.92[EUR][1000 genomes]
rs1915544	0.89[EUR][1000 genomes]
rs1996729	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs1996731	0.84[CEU][hapmap];0.93[EUR][1000 genomes]
rs1996732	0.93[EUR][1000 genomes]
rs2460997	0.88[EUR][1000 genomes]
rs2495396	0.85[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs35077383	0.93[EUR][1000 genomes]
rs35834074	0.98[EUR][1000 genomes]
rs4240870	0.93[EUR][1000 genomes]
rs4484926	0.84[CEU][hapmap];0.93[EUR][1000 genomes]
rs4634911	0.83[CEU][hapmap];0.93[EUR][1000 genomes]
rs4845355	0.96[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4845556	0.92[EUR][1000 genomes]
rs4995159	0.91[EUR][1000 genomes]
rs55982513	0.98[EUR][1000 genomes]
rs60136317	0.99[EUR][1000 genomes]
rs61815091	0.81[EUR][1000 genomes]
rs61815098	0.99[EUR][1000 genomes]
rs61815099	0.99[EUR][1000 genomes]
rs6587619	0.92[EUR][1000 genomes]
rs6672920	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs6680404	0.99[EUR][1000 genomes]
rs6684101	0.85[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs7521817	0.86[EUR][1000 genomes]
rs7523001	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7529549	0.91[EUR][1000 genomes]
rs868866	0.96[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs868867	0.96[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]

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	nsv1010398	chr1:151761649-151790940	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11586691	LYSMD1	cis	parietal	SCAN
rs11586691	CTSK	cis	cerebellum	SCAN
rs11586691	TDRKH	cis	cerebellum	SCAN
rs11586691	TDRKH	cis	parietal	SCAN
rs11586691	LCE2C	cis	parietal	SCAN
rs11586691	PLEKHO1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151764200-151772000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:151764200-151772800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:151764200-151772800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:151764200-151772800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:151764200-151773000	Weak transcription	Thymus	Thymus
6	chr1:151764200-151778800	Weak transcription	Pancreas	Pancrea
7	chr1:151764200-151779600	Weak transcription	Gastric	stomach
8	chr1:151764200-151787000	Weak transcription	Right Ventricle	heart
9	chr1:151764200-151792800	Weak transcription	Lung	lung
10	chr1:151764400-151779200	Weak transcription	Liver	Liver
11	chr1:151764400-151779800	Weak transcription	Brain Angular Gyrus	brain
12	chr1:151764600-151779400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:151764600-151779400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:151764600-151782000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:151764600-151787600	Weak transcription	Primary T cells from cord blood	blood
16	chr1:151765000-151772200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:151765000-151779400	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:151765400-151772800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:151765400-151784200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:151765800-151772000	Weak transcription	Fetal Brain Female	brain
21	chr1:151766000-151771800	Weak transcription	Brain Germinal Matrix	brain
22	chr1:151766000-151772600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:151766000-151780200	Weak transcription	Dnd41	blood
24	chr1:151770400-151776200	Weak transcription	Spleen	Spleen
25	chr1:151770800-151787200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:151771200-151772400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:151771400-151771800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:151771400-151771800	Active TSS	Brain Anterior Caudate	brain
29	chr1:151771400-151772000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:151771400-151773400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr1:151771400-151773600	Enhancers	Fetal Thymus	thymus
32	chr1:151771400-151778200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:151771600-151771800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:151771600-151771800	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr1:151771600-151772000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:151771600-151772200	Genic enhancers	Brain Inferior Temporal Lobe	brain
37	chr1:151771600-151772400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr1:151771600-151772400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:151771600-151772400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr1:151771600-151772600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
41	chr1:151771600-151772800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr1:151771600-151773200	Enhancers	Placenta	Placenta

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