Variant report

Variant	rs1525749
Chromosome Location	chr11:73367729-73367730
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	chr11:73367690-73368417	K562	blood:	n/a	n/a
2	POLR2A	chr11:73367629-73368349	K562	blood:	n/a	n/a
3	POLR2A	chr11:73367631-73368417	K562	blood:	n/a	n/a
4	POLR2A	chr11:73367144-73367805	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:73367571-73368421	Hela-S3	cervix:	n/a	n/a
6	HEY1	chr11:73367598-73368442	K562	blood:	n/a	n/a
7	POLR2A	chr11:73367710-73368403	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:73366404..73368809-chr11:73373660..73375819,2	MCF-7	breast:
2	chr11:73307468..73310175-chr11:73367058..73369059,2	MCF-7	breast:
3	chr11:73366864..73370325-chr11:73372581..73375566,3	K562	blood:

Variant related genes	Relation type
PLEKHB1	TF binding region
ENSG00000252732	Chromatin interaction
ENSG00000054965	Chromatin interaction
ENSG00000021300	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10793063	0.80[ASN][1000 genomes]
rs10793064	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793065	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10898931	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs10898935	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs11235828	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11235830	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11235833	1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11235876	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap]
rs12420357	0.85[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs1670537	0.89[GIH][hapmap];0.83[TSI][hapmap]
rs1670557	0.84[GIH][hapmap]
rs1723843	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs1723848	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs1792156	0.89[GIH][hapmap];0.83[TSI][hapmap]
rs1792174	0.89[GIH][hapmap];0.83[TSI][hapmap]
rs1976911	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2008734	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2140893	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs3781909	0.92[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3817514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862797	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7103745	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7119055	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs868667	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]

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	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS 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 target site	85 gene(s)	inside rSNPs	diseases
4	nsv1045149	chr11:73314565-73581908	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv521125	chr11:73359236-73378142	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1525749	MRPL48	cis	cerebellum	SCAN
rs1525749	MRPL48	cis	lymphoblastoid	seeQTL
rs1525749	MRPL48	cis	multi-tissue	Pritchard
rs1525749	MRPL48	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73359000-73371600	Weak transcription	Fetal Brain Female	brain
2	chr11:73359000-73371600	Weak transcription	Right Ventricle	heart
3	chr11:73359200-73371600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:73359200-73371600	Weak transcription	Thymus	Thymus
5	chr11:73359200-73371800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr11:73359400-73371800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr11:73359600-73372200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr11:73359800-73371800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr11:73359800-73371800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:73361400-73367800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr11:73361800-73369200	Strong transcription	Primary T cells from cord blood	blood
12	chr11:73362000-73375000	Weak transcription	Aorta	Aorta
13	chr11:73363400-73370400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:73363400-73371600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr11:73363600-73370400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:73363600-73371800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:73363800-73368000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr11:73363800-73371600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:73363800-73385400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:73364000-73371400	Weak transcription	Fetal Intestine Small	intestine
21	chr11:73364000-73371800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:73364400-73368800	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:73364400-73371400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:73364400-73371600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr11:73364400-73371800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr11:73364400-73371800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr11:73364600-73371400	Weak transcription	Stomach Mucosa	stomach
28	chr11:73364600-73371600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:73364800-73371800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:73365400-73371600	Weak transcription	Osteobl	bone
31	chr11:73365400-73371800	Weak transcription	Right Atrium	heart
32	chr11:73365600-73368000	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr11:73365600-73369200	Strong transcription	Brain Cingulate Gyrus	brain
34	chr11:73365800-73371200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:73365800-73371600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:73366000-73369000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:73366000-73371400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr11:73366000-73371600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr11:73366000-73371800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:73366200-73371800	Weak transcription	Liver	Liver
41	chr11:73366400-73369800	Strong transcription	Brain Hippocampus Middle	brain
42	chr11:73366400-73369800	Strong transcription	Brain Substantia Nigra	brain
43	chr11:73366600-73369400	Strong transcription	HepG2	liver
44	chr11:73366600-73371800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:73366600-73371800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:73366800-73371600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr11:73367000-73371800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:73367200-73371000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:73367400-73368200	Weak transcription	Spleen	Spleen
50	chr11:73367400-73371600	Weak transcription	Gastric	stomach

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