Variant report

Variant	rs12429746
Chromosome Location	chr13:48616504-48616505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:48615997-48617008	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr13:48616474-48616504	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48611908..48615197-chr13:48616431..48620748,8	K562	blood:
2	chr13:48615412..48618304-chr13:48618924..48621110,2	K562	blood:

Variant related genes	Relation type
SUCLA2	TF binding region
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11838539	0.82[EUR][1000 genomes]
rs12427516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427964	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12428055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12428102	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12429099	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429105	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12429348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429993	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];0.87[ASN][1000 genomes]
rs12431130	0.82[EUR][1000 genomes]
rs1968029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2182374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2182375	0.82[ASN][1000 genomes]
rs2182377	0.82[ASN][1000 genomes]
rs2897496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35710390	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57698455	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57957392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58316588	0.82[EUR][1000 genomes]
rs58634823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61585711	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002322	0.82[ASN][1000 genomes]
rs840430	0.82[ASN][1000 genomes]
rs9534910	0.82[ASN][1000 genomes]
rs9534936	0.93[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	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
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48612400-48625000	Weak transcription	Spleen	Spleen
2	chr13:48612600-48623000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:48612600-48624200	Weak transcription	Gastric	stomach
4	chr13:48612600-48624800	Weak transcription	Ovary	ovary
5	chr13:48612600-48631600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:48612600-48640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr13:48612600-48645000	Weak transcription	Stomach Mucosa	stomach
8	chr13:48612800-48620800	Weak transcription	Primary B cells from cord blood	blood
9	chr13:48612800-48622000	Weak transcription	Brain Germinal Matrix	brain
10	chr13:48612800-48622000	Weak transcription	Placenta	Placenta
11	chr13:48612800-48622200	Weak transcription	Fetal Brain Female	brain
12	chr13:48612800-48622400	Weak transcription	Brain Substantia Nigra	brain
13	chr13:48612800-48624600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr13:48612800-48624800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr13:48612800-48625000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr13:48612800-48628000	Weak transcription	Fetal Brain Male	brain
17	chr13:48612800-48640200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr13:48612800-48640400	Weak transcription	Psoas Muscle	Psoas
19	chr13:48613000-48617600	Weak transcription	HSMMtube	muscle
20	chr13:48613000-48621800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr13:48613000-48622200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr13:48613000-48640200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr13:48613000-48640400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr13:48613200-48617400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr13:48613200-48624800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr13:48613200-48624800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr13:48613200-48626600	Weak transcription	Right Ventricle	heart
28	chr13:48613200-48629000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:48613200-48631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr13:48613200-48640400	Weak transcription	Fetal Heart	heart
31	chr13:48613200-48641600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr13:48613200-48642200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:48613400-48617400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr13:48613400-48617600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr13:48613400-48618200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr13:48613400-48624800	Weak transcription	Brain Anterior Caudate	brain
37	chr13:48613400-48625800	Weak transcription	K562	blood
38	chr13:48613400-48641600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr13:48613400-48647000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr13:48613600-48617600	Weak transcription	Colonic Mucosa	Colon
41	chr13:48613600-48622200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr13:48613600-48625200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr13:48613600-48636400	Weak transcription	Hela-S3	cervix
44	chr13:48613600-48645000	Weak transcription	Small Intestine	intestine
45	chr13:48614000-48616600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr13:48614200-48617200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr13:48614200-48617600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr13:48614400-48617400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:48614400-48618200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:48614400-48627600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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