Variant report

Variant	rs424955
Chromosome Location	chr5:52902895-52902896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10072971	0.83[EUR][1000 genomes]
rs10077935	0.83[ASN][1000 genomes]
rs1030228	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12521381	0.86[EUR][1000 genomes]
rs1465445	1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1532163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1552649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1559266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs173905	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1844696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1844698	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs187659	0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs198941	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2130744	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256083	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256085	0.87[ASN][1000 genomes]
rs256087	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256090	0.94[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs256097	0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs256100	0.81[ASN][1000 genomes]
rs256107	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256108	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256110	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256112	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256113	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256116	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs256117	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607501	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607502	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2607509	0.83[ASN][1000 genomes]
rs2607511	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636991	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636999	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2637004	0.87[ASN][1000 genomes]
rs2637027	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2637030	0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs271213	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs271217	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs31302	0.90[CHD][hapmap];0.86[GIH][hapmap];0.83[ASN][1000 genomes]
rs31303	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs370594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs372006	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs372135	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs375956	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs376566	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs381374	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs399141	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs403207	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147740	0.88[CEU][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs423014	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs423872	0.90[CHD][hapmap];0.86[GIH][hapmap];0.83[ASN][1000 genomes]
rs429384	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs430427	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs435187	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs439552	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs439641	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs449160	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs549131	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6881928	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7728496	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7731940	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs786333	0.83[ASN][1000 genomes]
rs786335	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs813301	0.83[ASN][1000 genomes]
rs889291	0.89[JPT][hapmap]
rs889292	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs923609	0.94[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[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	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	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv881348	chr5:52885100-52942083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv881237	chr5:52885100-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv880426	chr5:52885100-52953048	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv881604	chr5:52885100-53035301	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv880762	chr5:52894276-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv4828	chr5:52895470-52940279	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs424955	NDUFS4	cis	parietal	SCAN
rs424955	GPBP1	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52860000-52909000	Weak transcription	Small Intestine	intestine
2	chr5:52876800-52907400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:52885800-52906000	Weak transcription	Psoas Muscle	Psoas
4	chr5:52888000-52905000	Weak transcription	Right Ventricle	heart
5	chr5:52888800-52908200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:52889000-52904200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:52889800-52920800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:52890000-52903000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:52890000-52912400	Weak transcription	K562	blood
10	chr5:52890200-52903000	Weak transcription	HSMMtube	muscle
11	chr5:52890200-52907200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:52890200-52920000	Weak transcription	HepG2	liver
13	chr5:52893400-52903400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:52894200-52905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:52897800-52904000	Weak transcription	NH-A	brain
16	chr5:52897800-52904200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:52897800-52906200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:52898800-52904200	Weak transcription	Thymus	Thymus
19	chr5:52899000-52904200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:52899000-52904600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr5:52899200-52903200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:52899200-52903200	Weak transcription	NHDF-Ad	bronchial
23	chr5:52899200-52904000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:52899200-52904000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr5:52899200-52904400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr5:52899200-52904400	Weak transcription	Colonic Mucosa	Colon
27	chr5:52899200-52904800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:52899200-52905800	Weak transcription	Fetal Brain Female	brain
29	chr5:52899200-52906000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr5:52899200-52908400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr5:52899200-52908400	Weak transcription	HMEC	breast
32	chr5:52899200-52910200	Weak transcription	Brain Germinal Matrix	brain
33	chr5:52899400-52904000	Weak transcription	Ovary	ovary
34	chr5:52899400-52905600	Weak transcription	NHLF	lung
35	chr5:52899400-52908200	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:52899400-52908200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr5:52899400-52908400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr5:52899400-52908400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:52899400-52928400	Weak transcription	Fetal Heart	heart
40	chr5:52899800-52903000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:52899800-52903200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:52899800-52903200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr5:52899800-52903600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr5:52899800-52904600	Strong transcription	Adipose Nuclei	Adipose
45	chr5:52899800-52905000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:52899800-52905600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr5:52899800-52906400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr5:52900000-52906200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr5:52900200-52903000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:52900200-52903200	Strong transcription	Placenta	Placenta

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