Variant report

Variant	rs10908462
Chromosome Location	chr1:155285854-155285855
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	chr1:155285762-155295040	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:155285720-155292259	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr1:155285784-155285862	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155246729..155248789-chr1:155285548..155288546,2	K562	blood:
2	chr1:155247984..155249745-chr1:155285662..155287694,2	MCF-7	breast:

Variant related genes	Relation type
FDPS	TF binding region
RUSC1	TF binding region
ENSG00000143630	Chromatin interaction
ENSG00000176444	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1052176	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1052177	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10796941	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10908461	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10908463	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11264355	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11264357	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11264358	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11264359	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11264360	0.83[EUR][1000 genomes]
rs11264361	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12032720	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12044063	0.84[EUR][1000 genomes]
rs12067675	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12724449	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12749306	0.81[EUR][1000 genomes]
rs2071053	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2297480	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3020781	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3814318	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3814319	0.82[AMR][1000 genomes]
rs4620533	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6672284	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7524950	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7534795	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7549276	0.80[AMR][1000 genomes]
rs7554780	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8177968	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8847	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs932972	0.87[AMR][1000 genomes];0.83[EUR][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	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
2	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
3	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
4	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
5	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
6	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10908462	GBAP1	cis	Artery Tibial	GTEx
rs10908462	THBS3	cis	Whole Blood	GTEx
rs10908462	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs10908462	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs10908462	GBA	cis	Esophagus Mucosa	GTEx
rs10908462	GBAP1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155279200-155290400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:155279800-155290400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:155280000-155286800	Weak transcription	Brain Anterior Caudate	brain
4	chr1:155280000-155287200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:155280000-155287800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:155280000-155290000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:155280000-155290200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:155280000-155290200	Weak transcription	Right Atrium	heart
9	chr1:155280000-155290400	Weak transcription	Psoas Muscle	Psoas
10	chr1:155280200-155288200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:155280200-155289800	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr1:155280200-155289800	Strong transcription	Fetal Stomach	stomach
13	chr1:155280200-155290000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:155280600-155289800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:155280600-155289800	Weak transcription	Fetal Brain Male	brain
18	chr1:155280600-155290200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:155280600-155290200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:155280800-155290000	Strong transcription	Fetal Thymus	thymus
21	chr1:155280800-155290600	Weak transcription	Small Intestine	intestine
22	chr1:155281200-155286000	Strong transcription	Liver	Liver
23	chr1:155281200-155289200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:155281400-155288000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:155281400-155290600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:155281600-155287800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:155281600-155290200	Weak transcription	Stomach Mucosa	stomach
28	chr1:155281600-155290600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:155281800-155290000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:155282000-155289600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:155282200-155287600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:155282200-155287800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:155282200-155289800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:155282200-155290200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:155282200-155290600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:155282400-155289000	Strong transcription	HUVEC	blood vessel
37	chr1:155282400-155289200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:155282600-155288200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:155282800-155289800	Strong transcription	Fetal Brain Female	brain
40	chr1:155283000-155288800	Strong transcription	HMEC	breast
41	chr1:155283400-155286600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:155283400-155287800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:155283400-155288000	Weak transcription	Fetal Kidney	kidney
44	chr1:155283400-155288400	Weak transcription	Fetal Lung	lung
45	chr1:155283400-155290200	Weak transcription	Primary B cells from cord blood	blood
46	chr1:155283600-155286600	Weak transcription	A549	lung
47	chr1:155283600-155287200	Weak transcription	Osteobl	bone
48	chr1:155283600-155287800	Weak transcription	Gastric	stomach
49	chr1:155283600-155288000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:155283600-155289800	Weak transcription	Fetal Heart	heart

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