Variant report

Variant	rs1538648
Chromosome Location	chr10:94820860-94820861
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	MAX	chr10:94820404-94821057	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr10:94819838-94821062	H1-hESC	embryonic stem cell:	n/a	chr10:94820319-94820329 chr10:94820375-94820385
3	MAX	chr10:94820575-94821034	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr10:94819717-94824643	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr10:94820661-94821007	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr10:94820840-94821162	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr10:94820487-94822020	K562	blood:	n/a	n/a

Variant related genes	Relation type
CYP26C1	TF binding region
ENSG00000226425	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10882124	0.90[JPT][hapmap]
rs1097215	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11187206	0.90[JPT][hapmap]
rs12771031	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326329	0.85[ASN][1000 genomes]
rs1536329	0.85[ASN][1000 genomes]
rs2478232	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2486689	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2486690	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4919038	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs61863078	0.82[ASN][1000 genomes]
rs68040629	1.00[ASN][1000 genomes]
rs7918909	0.90[JPT][hapmap]
rs835250	0.85[ASN][1000 genomes]
rs835259	0.86[ASN][1000 genomes]
rs835267	0.86[ASN][1000 genomes]
rs860668	0.85[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	esv1802015	chr10:94811983-94839960	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv895899	chr10:94818382-94836435	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1538648	SLC16A12	cis	cerebellum	SCAN
rs1538648	TLL2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94804200-94821000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr10:94806200-94821000	Weak transcription	Gastric	stomach
3	chr10:94808000-94821000	Weak transcription	Pancreas	Pancrea
4	chr10:94811800-94825000	Weak transcription	HepG2	liver
5	chr10:94816600-94821200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr10:94817600-94821200	Strong transcription	Dnd41	blood
7	chr10:94818000-94822800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr10:94818400-94821200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr10:94818400-94821200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr10:94818800-94821000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr10:94818800-94821000	Weak transcription	A549	lung
12	chr10:94819400-94821600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr10:94819600-94821200	ZNF genes & repeats	Lung	lung
14	chr10:94819600-94821400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr10:94819600-94821400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr10:94819600-94821800	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr10:94819600-94822200	Bivalent Enhancer	Fetal Intestine Large	intestine
18	chr10:94819600-94823600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr10:94819800-94821200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr10:94819800-94821400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
21	chr10:94819800-94821400	Bivalent Enhancer	Adipose Nuclei	Adipose
22	chr10:94819800-94821400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
23	chr10:94819800-94821600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
24	chr10:94819800-94821800	Bivalent Enhancer	Liver	Liver
25	chr10:94819800-94821800	Bivalent Enhancer	Esophagus	oesophagus
26	chr10:94819800-94822000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr10:94819800-94822000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr10:94819800-94822200	Bivalent Enhancer	Fetal Intestine Small	intestine
29	chr10:94819800-94823600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr10:94819800-94827800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr10:94820000-94821000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr10:94820000-94821200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
33	chr10:94820000-94821400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr10:94820000-94821600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:94820000-94821800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr10:94820000-94821800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr10:94820000-94821800	Weak transcription	HUVEC	blood vessel
38	chr10:94820000-94823600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
39	chr10:94820200-94821400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr10:94820200-94821800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr10:94820200-94822000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
42	chr10:94820200-94822600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr10:94820400-94821000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
44	chr10:94820400-94821000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
45	chr10:94820400-94821600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr10:94820400-94821800	Bivalent Enhancer	Right Ventricle	heart
47	chr10:94820400-94822800	Bivalent Enhancer	Placenta	Placenta
48	chr10:94820400-94823400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
49	chr10:94820600-94821000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
50	chr10:94820600-94821200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell

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