Variant report

Variant	rs13101418
Chromosome Location	chr4:78875974-78875975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78875922..78877424-chr4:78879284..78881268,2	MCF-7	breast:
2	chr4:78875058..78877167-chr4:78886944..78889062,2	K562	blood:

Variant related genes	Relation type
ENSG00000248926	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10033527	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10033613	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1021824	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1021826	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097938	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs11729215	0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs12641050	0.90[ASN][1000 genomes]
rs12645742	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs13101987	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs13103035	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs13103523	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs13106067	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13114091	0.90[ASN][1000 genomes]
rs13120272	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs16996915	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs17002807	0.86[YRI][hapmap]
rs17002849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2088992	0.83[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap]
rs2088994	0.87[ASN][1000 genomes]
rs2102191	0.86[ASN][1000 genomes]
rs28404443	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34459497	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34751953	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34850103	0.90[ASN][1000 genomes]
rs35648590	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35979107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4453957	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4571357	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4577601	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859509	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4859511	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859877	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs4859879	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4859888	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859889	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61207396	0.87[ASN][1000 genomes]
rs62302728	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62302732	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62310785	0.87[ASN][1000 genomes]
rs6533282	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6533291	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6533344	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533345	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66825464	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6811736	0.86[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6814912	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6845998	0.90[ASN][1000 genomes]
rs6848029	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6854895	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7670157	0.86[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7675009	0.81[CEU][hapmap];0.91[CHB][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap]
rs7676660	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7695874	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7698627	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7698629	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs905376	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
4	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13101418	MRPL1	cis	lymphoblastoid	seeQTL
rs13101418	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs13101418	MRPL1	Cis_1M	lymphoblastoid	RTeQTL
rs13101418	FRAS1	cis	parietal	SCAN
rs13101418	HMGB1P44	cis	Muscle Skeletal	GTEx
rs13101418	MRPL1	cis	cerebellum	SCAN
rs13101418	C4orf26	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:78809600-78881200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:78816400-78876000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:78830400-78877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:78849400-78876600	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:78849600-78881000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:78850200-78881000	Weak transcription	A549	lung
8	chr4:78852000-78881200	Weak transcription	Lung	lung
9	chr4:78852600-78878200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:78853200-78878000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:78853200-78880800	Weak transcription	Osteobl	bone
12	chr4:78853200-78881000	Weak transcription	Brain Anterior Caudate	brain
13	chr4:78853800-78876400	Weak transcription	Fetal Heart	heart
14	chr4:78853800-78877600	Weak transcription	NHEK	skin
15	chr4:78854200-78877800	Weak transcription	HSMMtube	muscle
16	chr4:78859400-78879000	Weak transcription	Small Intestine	intestine
17	chr4:78860000-78877800	Weak transcription	Esophagus	oesophagus
18	chr4:78860600-78877400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:78863400-78880800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:78864000-78876400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:78865600-78876600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:78865600-78877600	Weak transcription	Fetal Stomach	stomach
23	chr4:78865800-78881000	Weak transcription	Psoas Muscle	Psoas
24	chr4:78866800-78877800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:78866800-78881000	Weak transcription	Fetal Kidney	kidney
26	chr4:78867200-78877600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:78867600-78876400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:78868600-78881000	Weak transcription	Brain Angular Gyrus	brain
29	chr4:78869000-78879600	Weak transcription	Spleen	Spleen
30	chr4:78869600-78877600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:78870200-78876200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr4:78870400-78877200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:78870400-78881000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:78870600-78876600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr4:78870800-78876400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:78870800-78876600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr4:78871000-78876200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:78871000-78876200	Strong transcription	Liver	Liver
39	chr4:78871000-78878000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:78871000-78878600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:78871200-78876000	Strong transcription	Fetal Lung	lung
42	chr4:78871200-78876200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr4:78871200-78876200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr4:78871200-78876400	Strong transcription	Primary B cells from cord blood	blood
45	chr4:78871200-78876400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:78871400-78876200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:78871400-78876200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:78871400-78876200	Strong transcription	Adipose Nuclei	Adipose
49	chr4:78871400-78876200	Strong transcription	HUVEC	blood vessel
50	chr4:78871600-78876200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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