Variant report

Variant	rs10796941
Chromosome Location	chr1:155284261-155284262
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	chr1:155283979-155285177	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr1:155284048-155285704	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155264765..155268361-chr1:155281187..155284828,3	K562	blood:
2	chr1:155246251..155249792-chr1:155281813..155284527,3	K562	blood:
3	chr1:155276713..155281137-chr1:155281789..155284748,5	MCF-7	breast:
4	chr1:155247177..155249035-chr1:155283862..155285700,2	MCF-7	breast:

Variant related genes	Relation type
FDPS	TF binding region
ENSG00000143630	Chromatin interaction
ENSG00000176444	Chromatin interaction
ENSG00000160752	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1052176	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1052177	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10908461	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10908462	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10908463	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264349	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11264352	0.81[EUR][1000 genomes]
rs11264353	0.81[EUR][1000 genomes]
rs11264354	0.80[EUR][1000 genomes]
rs11264355	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11264357	0.84[EUR][1000 genomes]
rs11264358	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264359	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264360	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11264361	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12032720	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12044063	0.86[EUR][1000 genomes]
rs12049375	0.81[EUR][1000 genomes]
rs12067675	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12724449	0.83[EUR][1000 genomes]
rs12749306	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2071053	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2297480	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3020781	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3814318	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4620533	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4971072	0.85[ASN][1000 genomes]
rs6672284	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7520184	0.81[EUR][1000 genomes]
rs7524950	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7534795	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7549276	0.81[EUR][1000 genomes]
rs7554780	0.82[EUR][1000 genomes]
rs8177968	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8847	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs932972	0.86[AMR][1000 genomes];0.84[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10796941	PKLR	cis	Nerve Tibial	GTEx
rs10796941	GBAP1	cis	Artery Tibial	GTEx
rs10796941	GBA	cis	Esophagus Mucosa	GTEx
rs10796941	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs10796941	FDPS	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155279200-155290400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:155279800-155290400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:155280000-155285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:155280000-155286800	Weak transcription	Brain Anterior Caudate	brain
5	chr1:155280000-155287200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:155280000-155287800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:155280000-155290000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:155280000-155290200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:155280000-155290200	Weak transcription	Right Atrium	heart
10	chr1:155280000-155290400	Weak transcription	Psoas Muscle	Psoas
11	chr1:155280200-155285000	Strong transcription	Fetal Intestine Small	intestine
12	chr1:155280200-155288200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:155280200-155289800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr1:155280200-155289800	Strong transcription	Fetal Stomach	stomach
15	chr1:155280200-155290000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:155280400-155285200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:155280400-155285200	Strong transcription	Thymus	Thymus
20	chr1:155280600-155285000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:155280600-155285200	Strong transcription	Esophagus	oesophagus
22	chr1:155280600-155285400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:155280600-155289800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:155280600-155289800	Weak transcription	Fetal Brain Male	brain
25	chr1:155280600-155290200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:155280600-155290200	Weak transcription	Brain Substantia Nigra	brain
27	chr1:155280800-155285000	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:155280800-155285000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:155280800-155285000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:155280800-155290000	Strong transcription	Fetal Thymus	thymus
31	chr1:155280800-155290600	Weak transcription	Small Intestine	intestine
32	chr1:155281200-155285000	Strong transcription	Adipose Nuclei	Adipose
33	chr1:155281200-155285200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:155281200-155285200	Strong transcription	Lung	lung
35	chr1:155281200-155286000	Strong transcription	Liver	Liver
36	chr1:155281200-155289200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:155281400-155284400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:155281400-155285000	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr1:155281400-155285000	Genic enhancers	HepG2	liver
40	chr1:155281400-155285200	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr1:155281400-155285200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:155281400-155288000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:155281400-155290600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:155281600-155285000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:155281600-155285000	Strong transcription	Placenta	Placenta
46	chr1:155281600-155285200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:155281600-155287800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:155281600-155290200	Weak transcription	Stomach Mucosa	stomach
49	chr1:155281600-155290600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:155281800-155285000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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