Variant report

Variant	rs12429993
Chromosome Location	chr13:48532705-48532706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11838539	0.82[EUR][1000 genomes]
rs12427516	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12427964	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12428055	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12428102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12429099	0.90[EUR][1000 genomes]
rs12429105	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12429348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12429746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430076	0.85[AMR][1000 genomes]
rs12430172	0.85[AMR][1000 genomes]
rs12431057	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12431130	0.82[EUR][1000 genomes]
rs1968029	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2094191	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2148242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2182374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2182377	0.82[ASN][1000 genomes]
rs2897496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35710390	0.95[EUR][1000 genomes]
rs57698455	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57957392	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58316588	0.82[EUR][1000 genomes]
rs58634823	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61585711	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8002322	0.82[ASN][1000 genomes]
rs840430	0.82[ASN][1000 genomes]
rs9534910	0.82[ASN][1000 genomes]
rs9567962	0.94[ASN][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	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
2	chr13:48511000-48536600	Weak transcription	Esophagus	oesophagus
3	chr13:48512600-48537600	Weak transcription	Hela-S3	cervix
4	chr13:48512800-48533800	Weak transcription	NHLF	lung
5	chr13:48514400-48574000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr13:48519600-48533800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr13:48523000-48541600	Weak transcription	Psoas Muscle	Psoas
8	chr13:48523000-48542600	Weak transcription	K562	blood
9	chr13:48523200-48534000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr13:48523200-48536600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr13:48526400-48533600	Weak transcription	Right Ventricle	heart
12	chr13:48528000-48545800	Weak transcription	Colon Smooth Muscle	Colon
13	chr13:48528600-48541000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr13:48529200-48537200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr13:48529400-48537000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr13:48529400-48540200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr13:48529600-48535800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:48529800-48532800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr13:48529800-48532800	ZNF genes & repeats	GM12878-XiMat	blood
20	chr13:48529800-48533400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr13:48530000-48532800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
22	chr13:48530000-48535200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
23	chr13:48530000-48537200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
24	chr13:48530000-48538400	ZNF genes & repeats	Dnd41	blood
25	chr13:48530000-48541000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:48530000-48541200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr13:48530200-48533000	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr13:48530400-48534200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
29	chr13:48530600-48532800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
30	chr13:48530600-48534000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr13:48530600-48534200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr13:48530600-48534400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr13:48530600-48537200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
34	chr13:48530600-48538400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
35	chr13:48530600-48538800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
36	chr13:48530600-48540200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr13:48530600-48540400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
38	chr13:48530800-48534200	ZNF genes & repeats	Fetal Kidney	kidney
39	chr13:48531000-48533000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr13:48531000-48533600	Weak transcription	Fetal Brain Male	brain
41	chr13:48531000-48533800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr13:48531000-48536800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr13:48531600-48532800	Strong transcription	Osteobl	bone
44	chr13:48531800-48532800	Strong transcription	Brain Substantia Nigra	brain
45	chr13:48531800-48534000	Weak transcription	Spleen	Spleen
46	chr13:48531800-48536600	Weak transcription	Pancreas	Pancrea
47	chr13:48532000-48532800	Strong transcription	Placenta	Placenta
48	chr13:48532000-48533200	Strong transcription	NH-A	brain
49	chr13:48532000-48533600	Weak transcription	Small Intestine	intestine
50	chr13:48532000-48536800	Weak transcription	Colonic Mucosa	Colon

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