Variant report

Variant	rs4240871
Chromosome Location	chr1:154202735-154202736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154201106..154203777-chr1:154208596..154211363,2	K562	blood:
2	chr1:154155761..154157503-chr1:154201763..154204378,2	K562	blood:
3	chr1:154200748..154203473-chr1:154220403..154223108,2	MCF-7	breast:
4	chr1:154201393..154203526-chr1:154206473..154209093,2	MCF-7	breast:
5	chr1:154202277..154205016-chr1:154208534..154211363,2	K562	blood:
6	chr1:154201626..154203507-chr1:154214139..154215846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143569	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10158820	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1044013	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10797047	0.91[ASN][1000 genomes]
rs11265251	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265299	0.81[EUR][1000 genomes]
rs1194593	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1194596	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12023901	0.85[ASN][1000 genomes]
rs12025237	0.86[ASN][1000 genomes]
rs12026615	0.86[ASN][1000 genomes]
rs12027999	0.86[ASN][1000 genomes]
rs12028554	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12029331	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12062977	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12408458	0.81[EUR][1000 genomes]
rs12733060	0.86[ASN][1000 genomes]
rs12738393	0.86[ASN][1000 genomes]
rs1760802	0.83[ASN][1000 genomes]
rs1760803	0.81[ASN][1000 genomes]
rs1986709	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274993	0.86[ASN][1000 genomes]
rs2282227	0.82[ASN][1000 genomes]
rs2340473	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2879788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762339	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762340	0.83[ASN][1000 genomes]
rs3790613	0.86[ASN][1000 genomes]
rs3790614	0.86[ASN][1000 genomes]
rs3811453	0.81[ASN][1000 genomes]
rs3828076	0.81[EUR][1000 genomes]
rs3828077	0.86[ASN][1000 genomes]
rs6427509	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657214	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6673752	0.86[ASN][1000 genomes]
rs6719	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517578	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7524346	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7551128	0.81[EUR][1000 genomes]
rs9803857	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9943093	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	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
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4240871	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	chr1:154195200-154211400	Weak transcription	Right Atrium	heart
2	chr1:154195400-154234600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:154195600-154244000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:154195800-154204000	Weak transcription	Stomach Mucosa	stomach
5	chr1:154196200-154203200	Weak transcription	Fetal Brain Male	brain
6	chr1:154196200-154243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:154196400-154218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:154196400-154243800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:154196600-154237600	Strong transcription	Fetal Thymus	thymus
10	chr1:154196600-154243600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:154196800-154211800	Strong transcription	NHEK	skin
12	chr1:154196800-154224200	Strong transcription	K562	blood
13	chr1:154196800-154224400	Strong transcription	Primary B cells from cord blood	blood
14	chr1:154196800-154235800	Strong transcription	HUVEC	blood vessel
15	chr1:154196800-154242600	Strong transcription	A549	lung
16	chr1:154197000-154235000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:154197000-154242800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:154197200-154205000	Strong transcription	NHDF-Ad	bronchial
23	chr1:154197200-154210800	Strong transcription	HMEC	breast
24	chr1:154197200-154214200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:154197400-154203400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:154197400-154212200	Strong transcription	Stomach Smooth Muscle	stomach
29	chr1:154197400-154224200	Strong transcription	Hela-S3	cervix
30	chr1:154197400-154242800	Strong transcription	Brain Anterior Caudate	brain
31	chr1:154197600-154202800	Strong transcription	Spleen	Spleen
32	chr1:154197600-154203600	Strong transcription	NH-A	brain
33	chr1:154197600-154204400	Strong transcription	HSMM	muscle
34	chr1:154197600-154204600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:154197600-154205200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:154197600-154205400	Strong transcription	Fetal Lung	lung
37	chr1:154197600-154205800	Strong transcription	Rectal Smooth Muscle	rectum
38	chr1:154197600-154208800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:154197600-154209600	Strong transcription	Fetal Intestine Small	intestine
40	chr1:154197600-154210600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:154197600-154211200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:154197600-154211200	Strong transcription	Lung	lung
43	chr1:154197600-154212800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:154197600-154213200	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr1:154197600-154214000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:154197600-154214600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:154197600-154218600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:154197600-154218800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:154197600-154226400	Strong transcription	Osteobl	bone
50	chr1:154197600-154236000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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