Variant report

Variant	rs10797047
Chromosome Location	chr1:154149240-154149241
allele	A/G
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	chr1:154148249-154149321	PFSK-1	brain:	n/a	n/a
2	STAT3	chr1:154149034-154149350	MCF10A-Er-Src	breast:	n/a	chr1:154149035-154149046

No.	Distal block	Cell Line	Cell type
1	chr1:154145134..154153289-chr1:154153487..154160631,22	K562	blood:
2	chr1:153961925..153965410-chr1:154146555..154149414,3	MCF-7	breast:
3	chr1:154142747..154146273-chr1:154146772..154152940,5	K562	blood:
4	chr1:154138203..154141121-chr1:154149226..154151416,2	MCF-7	breast:
5	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
6	chr1:154148286..154150697-chr1:154192561..154194921,2	MCF-7	breast:

Variant related genes	Relation type
TPM3	TF binding region
ENSG00000143549	Chromatin interaction
ENSG00000264384	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000143569	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10158820	0.90[ASN][1000 genomes]
rs1044013	0.86[ASN][1000 genomes]
rs11265251	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1194593	0.88[ASN][1000 genomes]
rs1194596	0.88[ASN][1000 genomes]
rs12028554	0.88[ASN][1000 genomes]
rs12029331	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12062977	0.90[ASN][1000 genomes]
rs12568280	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1986709	0.88[ASN][1000 genomes]
rs2340473	0.90[ASN][1000 genomes]
rs2879788	0.91[ASN][1000 genomes]
rs3762339	0.90[ASN][1000 genomes]
rs4240871	0.91[ASN][1000 genomes]
rs60633748	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6427509	0.90[ASN][1000 genomes]
rs6657214	0.88[ASN][1000 genomes]
rs6719	0.91[ASN][1000 genomes]
rs7517578	0.87[ASN][1000 genomes]
rs9803857	0.88[ASN][1000 genomes]
rs9943093	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10797047	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154127000-154149600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:154127800-154150000	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr1:154128000-154150400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:154128000-154150800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:154128200-154150200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:154128200-154151200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:154129600-154149800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:154129600-154150400	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr1:154130200-154150600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:154130600-154149800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:154130600-154150000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:154133200-154149600	Strong transcription	A549	lung
13	chr1:154133200-154149800	Strong transcription	Thymus	Thymus
14	chr1:154133600-154149800	Strong transcription	Dnd41	blood
15	chr1:154133600-154150200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:154142400-154152000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:154143800-154153600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:154144200-154154400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:154145600-154150600	Weak transcription	Aorta	Aorta
20	chr1:154145800-154150000	Weak transcription	Right Ventricle	heart
21	chr1:154145800-154150200	Weak transcription	Brain Substantia Nigra	brain
22	chr1:154145800-154150200	Weak transcription	Fetal Brain Male	brain
23	chr1:154145800-154150200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:154145800-154150200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:154145800-154150600	Weak transcription	Ovary	ovary
26	chr1:154145800-154151200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:154145800-154153400	Weak transcription	Fetal Kidney	kidney
28	chr1:154146800-154151000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:154147000-154149400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:154147000-154151400	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr1:154147200-154149800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:154147200-154152400	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr1:154147800-154149400	Strong transcription	HepG2	liver
34	chr1:154147800-154152400	Genic enhancers	Primary monocytes fromperipheralblood	blood
35	chr1:154148000-154149600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:154148000-154149600	Genic enhancers	GM12878-XiMat	blood
37	chr1:154148000-154149800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr1:154148000-154150600	Genic enhancers	Primary B cells from cord blood	blood
39	chr1:154148000-154150800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr1:154148200-154149400	Genic enhancers	Fetal Intestine Small	intestine
41	chr1:154148200-154149600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr1:154148200-154150200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:154148200-154150200	Genic enhancers	Duodenum Mucosa	Duodenum
44	chr1:154148200-154150800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:154148200-154151000	Enhancers	Colonic Mucosa	Colon
46	chr1:154148200-154153800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr1:154148400-154149400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
48	chr1:154148400-154149600	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr1:154148400-154149800	Weak transcription	Fetal Heart	heart
50	chr1:154148400-154151000	Genic enhancers	Fetal Intestine Large	intestine

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