Variant report

Variant	rs2964131
Chromosome Location	chr5:5492718-5492719
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:5491954..5492906-chr5:6837341..6838159,2	K562	blood:
2	chr5:5485902..5487652-chr5:5492681..5494252,2	K562	blood:
3	chr5:5492168..5492979-chr5:5886820..5887455,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10063885	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12653733	0.80[CEU][hapmap]
rs1541799	0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2560297	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2560298	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2560299	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2560300	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2578500	0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2578549	0.85[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2578550	0.81[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2578552	0.89[ASW][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2578553	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2578554	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2578556	0.84[EUR][1000 genomes]
rs2578557	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2578558	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2578564	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2578565	0.90[TSI][hapmap]
rs2619827	0.83[EUR][1000 genomes]
rs2619844	0.83[EUR][1000 genomes]
rs2918253	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918260	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2918261	0.93[TSI][hapmap]
rs2964160	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3098377	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3111175	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61063822	0.81[EUR][1000 genomes]
rs6894118	0.88[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757981	chr5:5447098-5764620	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv2759319	chr5:5447098-5764620	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2964131	NDUFS6	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5433400-5495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:5458600-5495000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:5462400-5494600	Weak transcription	Colonic Mucosa	Colon
4	chr5:5463000-5493800	Weak transcription	Fetal Heart	heart
5	chr5:5465200-5493800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:5465200-5495000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:5468000-5494000	Weak transcription	Fetal Brain Male	brain
8	chr5:5475400-5494000	Weak transcription	Fetal Intestine Small	intestine
9	chr5:5475400-5495000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:5477000-5494000	Weak transcription	Psoas Muscle	Psoas
11	chr5:5477000-5494200	Weak transcription	Fetal Kidney	kidney
12	chr5:5477000-5494400	Weak transcription	Small Intestine	intestine
13	chr5:5477000-5494400	Weak transcription	NHLF	lung
14	chr5:5477000-5494600	Weak transcription	Right Ventricle	heart
15	chr5:5477200-5493800	Weak transcription	NHDF-Ad	bronchial
16	chr5:5477200-5497600	Weak transcription	Brain Angular Gyrus	brain
17	chr5:5481200-5494000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:5482000-5494000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:5482000-5494000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr5:5482000-5494200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:5482200-5494000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr5:5482200-5495000	Weak transcription	NHEK	skin
23	chr5:5482800-5497600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:5484000-5494000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:5484800-5493000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr5:5485200-5494600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:5487200-5494400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:5487400-5494600	Weak transcription	Brain Anterior Caudate	brain
29	chr5:5487400-5494600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:5487400-5495000	Weak transcription	Gastric	stomach
31	chr5:5487800-5494200	Weak transcription	Fetal Brain Female	brain
32	chr5:5488000-5494000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:5488000-5494400	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:5488200-5494400	Weak transcription	HUVEC	blood vessel
35	chr5:5488800-5493600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr5:5489600-5494000	Weak transcription	Spleen	Spleen
37	chr5:5489600-5494600	Weak transcription	Aorta	Aorta
38	chr5:5489600-5494600	Weak transcription	HepG2	liver
39	chr5:5489800-5494000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr5:5490000-5494000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr5:5490000-5494200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr5:5490200-5493600	Weak transcription	GM12878-XiMat	blood
43	chr5:5490200-5494000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:5490200-5494200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:5490200-5494600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:5490200-5494600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:5490200-5495000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:5490200-5495000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr5:5490400-5494000	Weak transcription	Left Ventricle	heart
50	chr5:5490400-5494200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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