Variant report

Variant	rs2653588
Chromosome Location	chr11:8947021-8947022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8941546..8948177-chr11:8950032..8955141,6	MCF-7	breast:
2	chr11:8940620..8943003-chr11:8946457..8949397,2	MCF-7	breast:
3	chr11:8718539..8720292-chr11:8944673..8947181,2	K562	blood:

Variant related genes	Relation type
ENSG00000176029	Chromatin interaction
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10840149	0.83[AFR][1000 genomes]
rs1980429	0.81[YRI][hapmap]
rs2455603	0.84[ASW][hapmap];0.93[LWK][hapmap];0.83[YRI][hapmap]
rs2568021	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs2568027	0.93[YRI][hapmap]
rs2653561	0.86[YRI][hapmap]
rs2653570	0.82[YRI][hapmap]
rs2653585	0.82[AFR][1000 genomes]
rs2653600	0.83[AFR][1000 genomes]
rs2653605	0.82[YRI][hapmap]
rs2742479	0.84[YRI][hapmap]
rs2742480	0.82[YRI][hapmap]
rs2742518	0.93[YRI][hapmap]
rs7396042	0.92[ASW][hapmap];0.93[LWK][hapmap];0.90[YRI][hapmap]
rs7925728	0.82[YRI][hapmap]
rs7932678	1.00[CHD][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2653588	C11orf17	cis	lymphoblastoid	seeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8933400-8947800	Weak transcription	Small Intestine	intestine
2	chr11:8934000-8952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:8934200-8948800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:8936400-8951200	Weak transcription	Right Atrium	heart
5	chr11:8936600-8948600	Strong transcription	Fetal Thymus	thymus
6	chr11:8936600-8949000	Strong transcription	Fetal Stomach	stomach
7	chr11:8936600-8954000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:8936800-8947600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr11:8937000-8947600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:8937000-8948200	Strong transcription	Fetal Brain Female	brain
11	chr11:8937200-8947400	Strong transcription	Thymus	Thymus
12	chr11:8937800-8947400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:8938000-8947400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:8938000-8947600	Strong transcription	Brain Cingulate Gyrus	brain
15	chr11:8938200-8947200	Strong transcription	Brain Germinal Matrix	brain
16	chr11:8939000-8947400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:8939000-8947600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:8939000-8948200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:8939400-8948200	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr11:8939400-8948800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:8939800-8947600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:8939800-8947600	Strong transcription	Lung	lung
23	chr11:8940000-8948400	Strong transcription	Spleen	Spleen
24	chr11:8940200-8948600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr11:8940200-8949200	Weak transcription	Primary B cells from cord blood	blood
26	chr11:8940400-8947200	Strong transcription	Fetal Muscle Leg	muscle
27	chr11:8940800-8947400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:8940800-8949200	Weak transcription	Fetal Heart	heart
29	chr11:8941200-8953400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr11:8941200-8956200	Weak transcription	K562	blood
31	chr11:8942000-8948800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:8942400-8950200	Weak transcription	Esophagus	oesophagus
33	chr11:8942400-8959000	Weak transcription	Fetal Kidney	kidney
34	chr11:8942600-8948800	Weak transcription	Colonic Mucosa	Colon
35	chr11:8943200-8950000	Weak transcription	GM12878-XiMat	blood
36	chr11:8943200-8950800	Weak transcription	Primary T cells from cord blood	blood
37	chr11:8943800-8969200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr11:8944000-8952200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr11:8944200-8956400	Weak transcription	HUVEC	blood vessel
40	chr11:8944600-8950000	Weak transcription	HMEC	breast
41	chr11:8944600-8950000	Weak transcription	HSMMtube	muscle
42	chr11:8944600-8950800	Weak transcription	HepG2	liver
43	chr11:8944600-8985000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:8944800-8949000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr11:8944800-8949200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr11:8944800-8949600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr11:8944800-8950200	Weak transcription	Placenta	Placenta
48	chr11:8944800-8954000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr11:8944800-8956400	Weak transcription	Fetal Intestine Large	intestine
50	chr11:8945000-8947200	Weak transcription	Rectal Mucosa Donor 29	rectum

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