Variant report

Variant	rs3102906
Chromosome Location	chr1:72488815-72488816
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:72488016..72488819-chr1:72503014..72503883,2	K562	blood:
2	chr1:72483188..72484849-chr1:72487728..72489377,2	K562	blood:
3	chr1:72487764..72489951-chr1:72495667..72497783,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1385915	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1486088	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486089	0.80[LWK][hapmap]
rs1486090	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs1486098	0.91[ASN][1000 genomes]
rs1486099	0.89[LWK][hapmap]
rs1486113	0.89[LWK][hapmap]
rs1872578	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1948061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422108	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630388	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630425	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs2801324	0.80[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2821282	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102903	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3102907	0.81[CHB][hapmap]
rs3102909	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102910	0.81[CHB][hapmap]
rs3102916	0.81[CHB][hapmap]
rs3102919	0.82[ASN][1000 genomes]
rs3128548	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3128549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3128553	0.81[CHB][hapmap]
rs3128557	0.89[LWK][hapmap]
rs3128558	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658032	0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6666863	0.89[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007910	chr1:72247302-72543998	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv428763	chr1:72353556-72499701	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1007073	chr1:72419858-72734657	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv546478	chr1:72442018-72512391	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1006076	chr1:72477436-72700903	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv534996	chr1:72477436-72700903	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3102906	ANKRD13C	cis	parietal	SCAN
rs3102906	IL13RA1	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72484600-72489600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:72484800-72490200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:72488400-72490800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr1:72488600-72489000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:72488600-72489000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:72488600-72489000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:72488600-72489000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:72488600-72489400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:72488600-72489600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:72488600-72489800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr1:72488800-72489000	Enhancers	H9 Cell Line	embryonic stem cell
12	chr1:72488800-72489200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr1:72488800-72489200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:72488800-72490800	Enhancers	Pancreatic Islets	Pancreatic Islet

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