Variant report

Variant	rs538627
Chromosome Location	chr11:63454732-63454733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:63439157..63441385-chr11:63453594..63455279,2	MCF-7	breast:
2	chr11:63447764..63451579-chr11:63451770..63456201,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184743	Chromatin interaction
ENSG00000133318	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1199383	1.00[AMR][1000 genomes]
rs1301131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17158455	1.00[YRI][hapmap]
rs17158456	0.85[YRI][hapmap]
rs2510524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2957251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2957254	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2957255	1.00[AMR][1000 genomes]
rs2957256	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2959888	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35375575	1.00[AMR][1000 genomes]
rs480271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs489327	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs489580	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs496346	1.00[AFR][1000 genomes]
rs496354	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs499942	0.85[YRI][hapmap]
rs501095	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs502017	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs502717	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs509932	1.00[YRI][hapmap]
rs512073	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs516068	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs516981	1.00[AMR][1000 genomes]
rs518304	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs518453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs519374	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs520640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs528770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs533130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs540034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs542124	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs554661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs560610	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56380757	1.00[AMR][1000 genomes]
rs569657	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs573083	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57478357	1.00[AMR][1000 genomes]
rs57658167	1.00[AMR][1000 genomes]
rs59235496	1.00[AMR][1000 genomes]
rs622400	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs653841	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs694024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv832183	chr11:63416678-63564565	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63449600-63455600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr11:63450400-63454800	Weak transcription	Gastric	stomach
3	chr11:63450400-63455200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:63450400-63456000	Weak transcription	Placenta	Placenta
5	chr11:63450400-63466400	Weak transcription	Small Intestine	intestine
6	chr11:63450600-63469200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:63450800-63460400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:63450800-63465400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:63450800-63465800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:63450800-63517400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr11:63451000-63466800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr11:63451000-63466800	Weak transcription	Stomach Mucosa	stomach
13	chr11:63451000-63467000	Weak transcription	Thymus	Thymus
14	chr11:63451200-63454800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:63451200-63455000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:63451200-63466400	Weak transcription	Fetal Intestine Large	intestine
17	chr11:63451200-63466800	Weak transcription	Fetal Kidney	kidney
18	chr11:63451200-63475000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr11:63451200-63478000	Weak transcription	HSMM	muscle
20	chr11:63451200-63486400	Weak transcription	Primary T cells from cord blood	blood
21	chr11:63451400-63455400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:63451400-63455400	Weak transcription	NHLF	lung
23	chr11:63451400-63455800	Enhancers	Fetal Brain Male	brain
24	chr11:63451400-63456400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:63451400-63457000	Weak transcription	HUVEC	blood vessel
26	chr11:63451400-63466800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr11:63451400-63478000	Weak transcription	HSMMtube	muscle
28	chr11:63451600-63455800	Enhancers	Adipose Nuclei	Adipose
29	chr11:63452000-63455400	Enhancers	Brain Germinal Matrix	brain
30	chr11:63452000-63486400	Weak transcription	Fetal Thymus	thymus
31	chr11:63452200-63455600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:63452200-63455600	Genic enhancers	Dnd41	blood
33	chr11:63452200-63456600	Weak transcription	HepG2	liver
34	chr11:63452400-63455800	Enhancers	Brain Substantia Nigra	brain
35	chr11:63452400-63458000	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr11:63452600-63469000	Weak transcription	Left Ventricle	heart
37	chr11:63452800-63455200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr11:63452800-63456800	Enhancers	K562	blood
39	chr11:63452800-63459400	Weak transcription	Fetal Stomach	stomach
40	chr11:63452800-63465400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:63452800-63466800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:63452800-63466800	Weak transcription	Lung	lung
43	chr11:63452800-63469000	Weak transcription	Fetal Intestine Small	intestine
44	chr11:63453000-63456000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:63453000-63459200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr11:63453000-63472800	Weak transcription	Pancreas	Pancrea
47	chr11:63453200-63455000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr11:63453200-63456600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:63453200-63457800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr11:63453200-63466800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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