Variant report

Variant	rs1030228
Chromosome Location	chr5:52842569-52842570
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	chr5:52836956..52838872-chr5:52840887..52843608,2	K562	blood:
2	chr5:52837372..52839534-chr5:52842108..52843861,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10057745	0.86[ASN][1000 genomes]
rs10063311	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10072971	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12521381	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1465445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532163	1.00[CEU][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1552649	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1559266	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1844696	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs1844698	0.80[EUR][1000 genomes]
rs187659	0.83[EUR][1000 genomes]
rs198941	0.94[CEU][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs2130744	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs256083	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs256087	1.00[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs256090	0.94[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs256095	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap]
rs256107	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs256108	1.00[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs256110	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs256112	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs256116	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap]
rs256117	1.00[CEU][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs2607511	0.82[EUR][1000 genomes]
rs2636991	0.83[EUR][1000 genomes]
rs2637027	0.80[EUR][1000 genomes]
rs31303	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs370594	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs372006	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs372135	0.83[EUR][1000 genomes]
rs375956	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs376566	0.80[EUR][1000 genomes]
rs381374	0.83[EUR][1000 genomes]
rs399141	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs403207	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4147740	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs423014	1.00[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs424955	1.00[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs429384	0.83[EUR][1000 genomes]
rs430427	0.83[EUR][1000 genomes]
rs435187	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs439552	1.00[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs439641	0.81[EUR][1000 genomes]
rs549131	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7728496	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7731940	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs786335	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs889291	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs889292	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs923609	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1030228	NDUFS4	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52837800-52843000	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr5:52838400-52843000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr5:52838800-52843000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:52838800-52843600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr5:52838800-52843600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:52839200-52843400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:52839200-52843400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:52839600-52842800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:52839600-52845600	Weak transcription	K562	blood
10	chr5:52840800-52843000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:52841000-52843000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr5:52841400-52843000	Enhancers	H1 Cell Line	embryonic stem cell
13	chr5:52841800-52842600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr5:52841800-52843400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr5:52842000-52843000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr5:52842200-52842800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:52842200-52843400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr5:52842200-52843600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:52842200-52843800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr5:52842400-52842800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:52842400-52843000	Enhancers	Liver	Liver
22	chr5:52842400-52843000	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links