Variant report

Variant	rs277414
Chromosome Location	chr5:41927423-41927424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:41927254..41930228-chr5:41945140..41947129,2	K562	blood:
2	chr5:41920030..41922138-chr5:41926101..41928998,2	MCF-7	breast:
3	chr5:41866693..41874585-chr5:41920680..41930326,14	K562	blood:
4	chr5:41923958..41925528-chr5:41925960..41928931,2	MCF-7	breast:
5	chr5:41903013..41905286-chr5:41924628..41927661,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151876	Chromatin interaction
ENSG00000205765	Chromatin interaction
ENSG00000083720	Chromatin interaction
ENSG00000248668	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10045473	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10051322	1.00[ASN][1000 genomes]
rs10059424	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10060170	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10062703	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10064298	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10064380	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10069638	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1006996	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070201	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10075064	0.90[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10077481	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10472357	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10941557	0.90[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1118104	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739257	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11740524	0.93[ASN][1000 genomes]
rs11744279	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11744516	0.81[ASN][1000 genomes]
rs11744623	0.93[ASN][1000 genomes]
rs11745373	0.90[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11747921	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1175227	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357951	1.00[ASN][1000 genomes]
rs13360001	0.90[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1355089	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1508816	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533014	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1567323	0.81[ASN][1000 genomes]
rs16871972	0.93[ASN][1000 genomes]
rs17739462	0.93[ASN][1000 genomes]
rs17847285	0.93[ASN][1000 genomes]
rs1876654	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2113053	1.00[ASN][1000 genomes]
rs2231910	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2231917	1.00[ASN][1000 genomes]
rs2329815	0.93[ASN][1000 genomes]
rs276315	0.95[GIH][hapmap];0.86[TSI][hapmap]
rs277406	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277407	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316724	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs316760	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34339137	0.93[ASN][1000 genomes]
rs34663371	0.93[ASN][1000 genomes]
rs35077044	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs35154057	0.93[ASN][1000 genomes]
rs35252930	0.81[ASN][1000 genomes]
rs35613904	0.93[ASN][1000 genomes]
rs4050986	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4289604	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324728	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4957171	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957173	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957174	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957175	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957176	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957177	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957178	1.00[ASN][1000 genomes]
rs4957180	1.00[ASN][1000 genomes]
rs4957422	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957423	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957424	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4957428	0.93[ASN][1000 genomes]
rs4957429	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957430	0.93[ASN][1000 genomes]
rs4957431	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957432	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957433	1.00[ASN][1000 genomes]
rs4957434	1.00[JPT][hapmap]
rs4957435	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957436	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957437	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957438	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957439	1.00[ASN][1000 genomes]
rs622413	0.85[EUR][1000 genomes]
rs624097	0.85[EUR][1000 genomes]
rs626907	1.00[JPT][hapmap]
rs6451581	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6451582	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66820325	0.93[ASN][1000 genomes]
rs67114999	0.93[ASN][1000 genomes]
rs676067	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881873	0.93[ASN][1000 genomes]
rs6889217	1.00[JPT][hapmap]
rs72746983	1.00[ASN][1000 genomes]
rs72746996	1.00[ASN][1000 genomes]
rs7712911	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7728482	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.81[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729014	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7733096	0.93[ASN][1000 genomes]
rs9292825	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762518	chr5:41780210-41935113	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases
2	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
3	nsv830273	chr5:41867296-42066070	Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
4	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
5	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs277414	C5orf39	cis	cerebellum	SCAN
rs277414	NUDC	trans	parietal	SCAN
rs277414	LIFR	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41926000-41935400	Weak transcription	Aorta	Aorta
2	chr5:41926000-41937600	Weak transcription	Fetal Brain Male	brain
3	chr5:41926000-41937600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:41926000-41940600	Weak transcription	Ovary	ovary
5	chr5:41926000-41951400	Weak transcription	Gastric	stomach
6	chr5:41926200-41928000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:41926200-41929400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:41926200-41929400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:41926200-41929800	Weak transcription	HMEC	breast
10	chr5:41926200-41930000	Enhancers	HepG2	liver
11	chr5:41926200-41931600	Weak transcription	Fetal Thymus	thymus
12	chr5:41926200-41931800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:41926200-41932800	Weak transcription	Small Intestine	intestine
14	chr5:41926200-41933200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:41926200-41934000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:41926200-41934000	Weak transcription	Placenta	Placenta
17	chr5:41926200-41934200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:41926200-41934200	Weak transcription	Brain Substantia Nigra	brain
19	chr5:41926200-41934200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr5:41926200-41934200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:41926200-41934200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:41926200-41935000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:41926200-41935400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:41926200-41935400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:41926200-41935400	Weak transcription	Brain Angular Gyrus	brain
26	chr5:41926200-41935400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:41926200-41935400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:41926200-41935400	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:41926200-41935400	Weak transcription	Fetal Stomach	stomach
30	chr5:41926200-41935400	Weak transcription	Left Ventricle	heart
31	chr5:41926200-41935400	Weak transcription	Lung	lung
32	chr5:41926200-41935400	Weak transcription	Psoas Muscle	Psoas
33	chr5:41926200-41935400	Weak transcription	Right Ventricle	heart
34	chr5:41926200-41936800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:41926200-41937200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:41926200-41937400	Weak transcription	Fetal Brain Female	brain
37	chr5:41926200-41937400	Weak transcription	Fetal Kidney	kidney
38	chr5:41926200-41939000	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:41926200-41940800	Weak transcription	HSMMtube	muscle
40	chr5:41926200-41940800	Weak transcription	NHDF-Ad	bronchial
41	chr5:41926200-41941000	Weak transcription	NHLF	lung
42	chr5:41926200-41943200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:41926200-41945000	Weak transcription	HSMM	muscle
44	chr5:41926200-41945200	Weak transcription	Esophagus	oesophagus
45	chr5:41926200-41945400	Weak transcription	Fetal Lung	lung
46	chr5:41926200-41946800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:41926200-41947000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:41926400-41929800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:41926400-41929800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:41926400-41929800	Weak transcription	Hela-S3	cervix

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