Variant report

Variant	rs11584327
Chromosome Location	chr1:10578791-10578792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10578631..10580602-chr1:11071261..11074067,2	MCF-7	breast:
2	chr1:10577532..10580475-chr1:10590665..10593408,2	K562	blood:
3	chr1:10576160..10578872-chr1:10926632..10929593,2	MCF-7	breast:
4	chr1:10570193..10573088-chr1:10575798..10579645,3	MCF-7	breast:
5	chr1:10576842..10579451-chr1:11119140..11122030,2	K562	blood:

Variant related genes	Relation type
ENSG00000120948	Chromatin interaction
ENSG00000116649	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10779737	0.90[EUR][1000 genomes]
rs11121579	0.81[CEU][hapmap]
rs11121581	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11580264	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12073943	0.86[EUR][1000 genomes]
rs12117392	1.00[YRI][hapmap]
rs12120962	1.00[YRI][hapmap]
rs12127400	0.84[MKK][hapmap];1.00[YRI][hapmap]
rs12565133	0.86[TSI][hapmap]
rs17035189	0.88[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1755592	0.87[EUR][1000 genomes]
rs2186949	0.82[EUR][1000 genomes]
rs2274985	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[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2781233	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs589151	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs602601	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs604369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs604814	0.96[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6688558	0.84[MKK][hapmap];1.00[YRI][hapmap]
rs670666	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[TSI][hapmap]
rs684016	0.84[TSI][hapmap]
rs7419116	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs7512495	0.89[YRI][hapmap]
rs7543322	0.88[CEU][hapmap];0.98[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs7548453	0.88[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7555790	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11584327	KIAA2013	cis	parietal	SCAN
rs11584327	APITD1	cis	cerebellum	SCAN
rs11584327	PLEKHG5	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10566800-10579800	Enhancers	Liver	Liver
2	chr1:10569000-10578800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:10570800-10579800	Weak transcription	Aorta	Aorta
4	chr1:10570800-10595600	Weak transcription	Primary B cells from cord blood	blood
5	chr1:10571400-10579400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:10571600-10579200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:10572000-10578800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:10572000-10579000	Weak transcription	A549	lung
9	chr1:10572000-10579000	Weak transcription	NH-A	brain
10	chr1:10572000-10590000	Weak transcription	Spleen	Spleen
11	chr1:10572200-10598600	Weak transcription	Brain Anterior Caudate	brain
12	chr1:10572600-10587600	Weak transcription	Hela-S3	cervix
13	chr1:10572600-10587800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:10573400-10596000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:10573800-10588000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:10573800-10588200	Weak transcription	Fetal Intestine Large	intestine
17	chr1:10574400-10579800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:10574600-10578800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:10574800-10580600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:10575600-10588000	Weak transcription	NHLF	lung
21	chr1:10576000-10578800	Weak transcription	HSMMtube	muscle
22	chr1:10576000-10579200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:10576000-10579200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr1:10576000-10579800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:10576000-10581600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:10576000-10589200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:10576400-10582000	Weak transcription	Thymus	Thymus
28	chr1:10576400-10582600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:10576400-10582600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:10576400-10596000	Weak transcription	Dnd41	blood
31	chr1:10576600-10579800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:10576600-10579800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:10576800-10579000	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr1:10576800-10579400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr1:10576800-10579800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:10576800-10579800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr1:10576800-10579800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:10576800-10582200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:10577000-10578800	Weak transcription	Fetal Heart	heart
40	chr1:10577000-10579000	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr1:10577000-10580000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr1:10577000-10603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:10577200-10579200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:10577200-10582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:10577200-10584600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:10577400-10578800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:10577400-10578800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:10577400-10578800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:10577400-10578800	Enhancers	Brain Germinal Matrix	brain
50	chr1:10577400-10578800	Weak transcription	Esophagus	oesophagus

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