Variant report

Variant	rs31127
Chromosome Location	chr5:53314757-53314758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:53313684..53316235-chr5:53319092..53322821,4	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs156836	0.94[GIH][hapmap];0.82[MEX][hapmap]
rs194281	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs255747	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs255748	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs255749	0.96[ASN][1000 genomes]
rs255750	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs255751	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs255753	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs255754	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs255758	0.94[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs255760	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs273223	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs274362	0.82[ASW][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs31226	0.90[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap]
rs373284	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs406517	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs426659	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs696007	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs697108	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs697109	0.82[ASW][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv830299	chr5:53207020-53386600	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv881265	chr5:53305742-53504764	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
8	nsv880619	chr5:53305742-53525671	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
9	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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	12 gene(s)	inside rSNPs	diseases
12	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
13	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
14	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
15	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs31127	NDUFS4	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53299200-53318000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:53308200-53316000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:53309800-53317600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:53310000-53317200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:53310400-53318000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:53310600-53316000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:53310600-53317400	Weak transcription	Osteobl	bone
8	chr5:53310600-53318000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:53310600-53318000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr5:53310600-53336000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:53310800-53317400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:53310800-53317400	Weak transcription	K562	blood
13	chr5:53310800-53318000	Weak transcription	Fetal Intestine Large	intestine
14	chr5:53311000-53317800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr5:53311200-53317400	Weak transcription	Fetal Intestine Small	intestine
16	chr5:53311400-53317200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr5:53311600-53316400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr5:53311600-53316600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr5:53311600-53317200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:53311600-53318000	Weak transcription	Spleen	Spleen
21	chr5:53311800-53316200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:53311800-53317800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr5:53312000-53317400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:53312000-53317800	Weak transcription	Adipose Nuclei	Adipose
25	chr5:53312800-53315200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:53313000-53314800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:53313000-53316000	Weak transcription	Lung	lung
28	chr5:53313000-53317400	Weak transcription	Primary T cells from cord blood	blood
29	chr5:53313200-53316000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:53313400-53316000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:53313400-53317400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:53313400-53317600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr5:53313600-53316000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr5:53313800-53315000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:53313800-53317400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr5:53314000-53314800	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr5:53314000-53314800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr5:53314200-53314800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:53314200-53315000	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr5:53314200-53315000	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr5:53314400-53315000	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr5:53314600-53315000	Active TSS	H1 Cell Line	embryonic stem cell
43	chr5:53314600-53315200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr5:53314600-53316400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:53314600-53321800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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