Variant report

Variant	rs11973006
Chromosome Location	chr7:40638365-40638366
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:40633290..40635892-chr7:40636595..40638399,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1000013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1019018	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10254954	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs10256576	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10263677	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs10429076	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486810	0.89[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10486811	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974322	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11977013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs11980464	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11982075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17171727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17171730	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17171747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1859705	0.84[ASN][1000 genomes]
rs2051919	0.92[CEU][hapmap]
rs2329819	0.89[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28657711	1.00[ASN][1000 genomes]
rs4720367	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4720371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4723967	0.91[LWK][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs4723972	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs61094306	0.82[EUR][1000 genomes]
rs61107746	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6462985	0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs66582232	0.94[EUR][1000 genomes]
rs66743443	0.90[EUR][1000 genomes]
rs67156695	0.87[EUR][1000 genomes]
rs67309967	0.87[EUR][1000 genomes]
rs67340458	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68082095	0.95[EUR][1000 genomes]
rs6943787	0.97[ASN][1000 genomes]
rs6945570	0.83[AFR][1000 genomes]
rs6948724	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954401	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap]
rs6956277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962853	0.95[EUR][1000 genomes]
rs6977104	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs73122188	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73308289	1.00[ASN][1000 genomes]
rs7459324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7776976	0.92[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7808612	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs917204	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9632613	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv887987	chr7:40505382-40748650	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv830971	chr7:40523075-40700172	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1025605	chr7:40623026-40789063	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv538823	chr7:40623026-40789063	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11973006	POLD2	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40635200-40639600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:40636400-40638400	Enhancers	HepG2	liver
3	chr7:40637200-40638600	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr7:40637600-40638600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:40637600-40639000	Enhancers	Dnd41	blood
6	chr7:40638000-40639400	Weak transcription	Aorta	Aorta
7	chr7:40638000-40641000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr7:40638000-40641000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:40638000-40641200	Enhancers	Primary hematopoietic stem cells	blood
10	chr7:40638200-40640200	Enhancers	Primary monocytes fromperipheralblood	blood

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