Variant report

Variant	rs4251540
Chromosome Location	chr12:44179579-44179580
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:44177060..44179217-chr12:44179398..44181923,2	K562	blood:
2	chr12:44170919..44172856-chr12:44178034..44180813,2	MCF-7	breast:
3	chr12:44177860..44183377-chr12:44197477..44201268,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151239	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10880559	0.96[ASN][1000 genomes]
rs10880560	1.00[ASN][1000 genomes]
rs10880561	0.84[ASN][1000 genomes]
rs11182232	1.00[CEU][hapmap]
rs11182235	1.00[CEU][hapmap]
rs11182236	1.00[CEU][hapmap]
rs11182244	1.00[CEU][hapmap]
rs11182250	1.00[CEU][hapmap]
rs12229685	1.00[CEU][hapmap]
rs12231953	0.82[CHB][hapmap]
rs1838341	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs3805198	0.86[AMR][1000 genomes]
rs4251425	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4251431	1.00[CEU][hapmap]
rs4251444	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4251446	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4251450	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4251463	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4251466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4251467	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4251473	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4251475	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4251487	0.81[EUR][1000 genomes]
rs4251489	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4251491	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4251493	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4251529	0.81[EUR][1000 genomes]
rs4251532	0.86[AMR][1000 genomes]
rs4251533	0.86[AMR][1000 genomes]
rs4251535	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4251538	0.81[EUR][1000 genomes]
rs4251539	0.81[EUR][1000 genomes]
rs4251545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4251555	0.84[AMR][1000 genomes]
rs4251574	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7311465	1.00[CEU][hapmap]
rs7313744	1.00[CEU][hapmap]
rs7954843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933142	chr12:44130156-44278300	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4251540	PUS7L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44154200-44189600	Weak transcription	Brain Angular Gyrus	brain
2	chr12:44154200-44189600	Weak transcription	A549	lung
3	chr12:44154200-44194400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:44154200-44199200	Weak transcription	Gastric	stomach
5	chr12:44154400-44181200	Weak transcription	Aorta	Aorta
6	chr12:44154400-44189400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:44154400-44189400	Weak transcription	Fetal Kidney	kidney
8	chr12:44154600-44189400	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:44154600-44199000	Weak transcription	Stomach Mucosa	stomach
10	chr12:44156600-44189400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:44158200-44182800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:44159000-44189000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:44159200-44188600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:44159400-44187200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:44160600-44182400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr12:44160600-44183600	Weak transcription	Fetal Heart	heart
17	chr12:44161200-44182400	Strong transcription	Primary hematopoietic stem cells	blood
18	chr12:44161600-44183400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:44161600-44183400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:44161800-44183800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:44162000-44183200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:44162000-44183200	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:44162200-44180800	Strong transcription	HSMM	muscle
24	chr12:44162200-44181600	Strong transcription	Liver	Liver
25	chr12:44162200-44182200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:44162200-44182200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr12:44162200-44182600	Strong transcription	Fetal Thymus	thymus
28	chr12:44162200-44182800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:44162200-44182800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:44163000-44182200	Strong transcription	Dnd41	blood
31	chr12:44165200-44180600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:44165400-44179800	Strong transcription	Osteobl	bone
33	chr12:44166600-44197200	Weak transcription	Fetal Brain Male	brain
34	chr12:44167600-44181600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr12:44167600-44182600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:44167600-44189600	Weak transcription	Hela-S3	cervix
37	chr12:44168000-44182600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:44168200-44182400	Strong transcription	Primary T cells from cord blood	blood
39	chr12:44168600-44189600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:44169400-44182000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:44169400-44189600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:44169400-44189800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr12:44170000-44182400	Strong transcription	GM12878-XiMat	blood
44	chr12:44170200-44180200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr12:44170200-44183200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:44170800-44181600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr12:44171000-44182200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:44171000-44182200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:44171200-44182200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr12:44171400-44182200	Strong transcription	Primary B cells from cord blood	blood

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