Variant report

Variant	rs55646648
Chromosome Location	chr11:45178890-45178891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45164428..45170441-chr11:45176063..45179885,12	MCF-7	breast:
2	chr11:45176255..45180138-chr11:45180420..45184771,5	MCF-7	breast:
3	chr11:45178718..45181474-chr11:45186088..45187942,2	K562	blood:
4	chr11:45175116..45179672-chr11:45200428..45203177,5	MCF-7	breast:
5	chr11:45166948..45170773-chr11:45176737..45181280,4	K562	blood:
6	chr11:45173226..45176543-chr11:45176880..45179156,4	K562	blood:

Variant related genes	Relation type
ENSG00000019485	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10444286	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10769123	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838428	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038341	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11038350	0.82[AMR][1000 genomes]
rs3886790	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907072	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825852	chr11:45141386-45228580	Bivalent/Poised TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv541025	chr11:45154352-45193352	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv1048493	chr11:45166054-45205695	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv523057	chr11:45174530-45181682	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55646648	SYT13	cis	Thyroid	GTEx
rs55646648	PRDM11	cis	Thyroid	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45169400-45181600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:45169800-45188000	Weak transcription	Primary T cells from cord blood	blood
3	chr11:45170000-45179000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr11:45170000-45179200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:45170000-45179400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr11:45170000-45190000	Weak transcription	Primary B cells from cord blood	blood
7	chr11:45170200-45179200	Weak transcription	Colonic Mucosa	Colon
8	chr11:45170200-45179400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:45170200-45179400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:45170400-45179000	Weak transcription	Brain Germinal Matrix	brain
11	chr11:45170400-45179600	Weak transcription	Fetal Brain Female	brain
12	chr11:45170400-45185200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr11:45170600-45179000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:45170600-45179400	Weak transcription	Psoas Muscle	Psoas
15	chr11:45170800-45179600	Weak transcription	Fetal Brain Male	brain
16	chr11:45170800-45180800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr11:45171200-45179200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:45172200-45179000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:45172400-45190000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:45174000-45179200	Weak transcription	Stomach Mucosa	stomach
21	chr11:45175400-45179000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:45175400-45182800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:45175600-45186200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr11:45176000-45181400	Enhancers	Right Ventricle	heart
25	chr11:45176000-45181400	Enhancers	Spleen	Spleen
26	chr11:45176000-45181600	Enhancers	Placenta	Placenta
27	chr11:45176000-45184200	Enhancers	Fetal Lung	lung
28	chr11:45176000-45186600	Genic enhancers	Fetal Stomach	stomach
29	chr11:45176200-45179600	Enhancers	HepG2	liver
30	chr11:45176200-45181800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr11:45176600-45183600	Enhancers	Esophagus	oesophagus
32	chr11:45177000-45179000	Weak transcription	Small Intestine	intestine
33	chr11:45177000-45179000	Genic enhancers	Stomach Smooth Muscle	stomach
34	chr11:45177000-45179200	Weak transcription	Adipose Nuclei	Adipose
35	chr11:45177000-45179800	Weak transcription	Aorta	Aorta
36	chr11:45177400-45180400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:45177600-45179200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:45177800-45180800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr11:45178000-45179200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:45178200-45181200	Enhancers	Ovary	ovary
41	chr11:45178200-45183600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:45178200-45187600	Enhancers	Fetal Heart	heart
43	chr11:45178400-45179000	Weak transcription	NHEK	skin
44	chr11:45178400-45179200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:45178400-45179200	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr11:45178400-45179600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:45178400-45180000	Enhancers	Colon Smooth Muscle	Colon
48	chr11:45178400-45181000	Enhancers	Duodenum Mucosa	Duodenum
49	chr11:45178400-45181400	Enhancers	Right Atrium	heart
50	chr11:45178400-45181800	Enhancers	Left Ventricle	heart

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