Variant report

Variant	rs17477129
Chromosome Location	chr13:49719060-49719061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:118790768..118792808-chr13:49718950..49721399,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1159972	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11617719	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11620305	0.82[EUR][1000 genomes]
rs12429554	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs61950730	0.81[EUR][1000 genomes]
rs73184687	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7990472	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	20 gene(s)	inside rSNPs	diseases
3	esv1796840	chr13:49671215-49760666	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1052168	chr13:49691378-49743696	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3411555	chr13:49718831-49719374	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17477129	SNORA31	cis	cerebellum	SCAN
rs17477129	TRIM13	cis	cerebellum	SCAN
rs17477129	CAB39L	cis	cerebellum	SCAN
rs17477129	KCNRG	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49687600-49724200	Weak transcription	Esophagus	oesophagus
2	chr13:49687600-49789000	Weak transcription	Stomach Mucosa	stomach
3	chr13:49693600-49737200	Weak transcription	Spleen	Spleen
4	chr13:49704400-49720000	Strong transcription	Dnd41	blood
5	chr13:49705000-49720400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr13:49705200-49720400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr13:49705200-49720600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:49705200-49720600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr13:49705200-49720600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr13:49705200-49721000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr13:49705200-49722400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr13:49705200-49723200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr13:49705400-49726600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr13:49705800-49737200	Weak transcription	Right Ventricle	heart
15	chr13:49706000-49737400	Weak transcription	Gastric	stomach
16	chr13:49706000-49748200	Weak transcription	K562	blood
17	chr13:49706200-49720800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr13:49706400-49721400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr13:49706600-49737000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr13:49706800-49737400	Weak transcription	Small Intestine	intestine
21	chr13:49707200-49721800	Weak transcription	Psoas Muscle	Psoas
22	chr13:49707400-49720800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr13:49707400-49724200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr13:49707800-49721000	Weak transcription	Brain Angular Gyrus	brain
25	chr13:49707800-49723400	Weak transcription	Fetal Brain Male	brain
26	chr13:49707800-49737200	Weak transcription	Lung	lung
27	chr13:49708000-49719800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr13:49708000-49720000	Weak transcription	Brain Hippocampus Middle	brain
29	chr13:49708000-49720600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr13:49708000-49721000	Weak transcription	A549	lung
31	chr13:49708000-49725800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:49709600-49737200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr13:49709800-49721400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr13:49709800-49721800	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr13:49710400-49720400	Strong transcription	Primary B cells from cord blood	blood
36	chr13:49711200-49724200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr13:49711400-49720400	Strong transcription	Liver	Liver
38	chr13:49711600-49737200	Weak transcription	Colonic Mucosa	Colon
39	chr13:49711800-49720600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr13:49711800-49725800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:49711800-49726600	Strong transcription	Placenta	Placenta
42	chr13:49711800-49736600	Weak transcription	Pancreas	Pancrea
43	chr13:49712000-49721000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr13:49712200-49719600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr13:49712200-49720000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr13:49712200-49720800	Weak transcription	NHLF	lung
47	chr13:49712200-49723800	Weak transcription	Ovary	ovary
48	chr13:49712200-49725600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr13:49712400-49720800	Weak transcription	Brain Anterior Caudate	brain
50	chr13:49712600-49719400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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