Variant report

Variant	rs277416
Chromosome Location	chr5:41926300-41926301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:41920030..41922138-chr5:41926101..41928998,2	MCF-7	breast:
2	chr5:41866693..41874585-chr5:41920680..41930326,14	K562	blood:
3	chr5:41924314..41927397-chr5:41938777..41942007,3	MCF-7	breast:
4	chr5:41924225..41926765-chr5:41937223..41939726,2	MCF-7	breast:
5	chr5:41923958..41925528-chr5:41925960..41928931,2	MCF-7	breast:
6	chr5:41864208..41872390-chr5:41920936..41926995,11	K562	blood:
7	chr11:62608643..62609927-chr5:41925312..41926323,3	Hela-S3	cervix:
8	chr5:41924171..41926713-chr5:43064683..43066902,2	K562	blood:
9	chr5:41903013..41905286-chr5:41924628..41927661,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000248668	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000151876	Chromatin interaction
ENSG00000205765	Chromatin interaction
ENSG00000083720	Chromatin interaction
ENSG00000172262	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];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[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];0.88[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	0.91[GIH][hapmap];0.86[TSI][hapmap]
rs277406	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277407	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277414	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];0.99[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
rs277416	NUDC	trans	parietal	SCAN
rs277416	LIFR	cis	cerebellum	SCAN
rs277416	C5orf39	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41924400-41926800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:41924600-41926400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:41924600-41926400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr5:41924800-41926400	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr5:41924800-41926400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:41924800-41926400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr5:41925000-41926400	Active TSS	Brain Anterior Caudate	brain
8	chr5:41925000-41926400	Active TSS	Fetal Intestine Large	intestine
9	chr5:41925000-41926400	Active TSS	Fetal Intestine Small	intestine
10	chr5:41925000-41926400	Active TSS	Thymus	Thymus
11	chr5:41925200-41926400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr5:41925200-41926400	Active TSS	Brain Hippocampus Middle	brain
13	chr5:41925200-41926400	Active TSS	Duodenum Mucosa	Duodenum
14	chr5:41925200-41926400	Active TSS	Rectal Smooth Muscle	rectum
15	chr5:41925200-41926400	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr5:41925200-41926400	Active TSS	NHEK	skin
17	chr5:41925200-41927200	Active TSS	K562	blood
18	chr5:41925400-41926600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:41925400-41926800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:41925400-41926800	Active TSS	GM12878-XiMat	blood
21	chr5:41925800-41926400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr5:41925800-41926400	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr5:41925800-41926400	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr5:41925800-41926400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr5:41925800-41926400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr5:41925800-41926400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr5:41925800-41926400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr5:41925800-41926400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr5:41925800-41926400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:41925800-41926400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr5:41925800-41926400	Flanking Active TSS	Hela-S3	cervix
32	chr5:41925800-41926400	Flanking Active TSS	HUVEC	blood vessel
33	chr5:41925800-41926400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr5:41925800-41927400	Flanking Active TSS	Dnd41	blood
35	chr5:41926000-41926400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:41926000-41926400	Flanking Active TSS	A549	lung
37	chr5:41926000-41926400	Flanking Active TSS	Osteobl	bone
38	chr5:41926000-41935400	Weak transcription	Aorta	Aorta
39	chr5:41926000-41937600	Weak transcription	Fetal Brain Male	brain
40	chr5:41926000-41937600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr5:41926000-41940600	Weak transcription	Ovary	ovary
42	chr5:41926000-41951400	Weak transcription	Gastric	stomach
43	chr5:41926200-41926400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:41926200-41926400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:41926200-41926400	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr5:41926200-41926400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr5:41926200-41926400	Active TSS	Muscle Satellite Cultured Cells	--
48	chr5:41926200-41926400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:41926200-41926400	Enhancers	Fetal Heart	heart
50	chr5:41926200-41926400	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links