Variant report

Variant	rs11974201
Chromosome Location	chr7:69334991-69334992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:69329979..69332138-chr7:69333837..69336630,2	K562	blood:
2	chr7:69334524..69336993-chr7:69356452..69358911,2	MCF-7	breast:
3	chr7:69333993..69336965-chr7:69341808..69343706,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1014417	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10245786	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10257549	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10259748	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10452738	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11508453	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11761141	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11763186	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11978431	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12333974	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12698813	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12698816	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12698822	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12698825	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12698830	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13226538	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13237811	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17140933	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17140980	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17140982	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs210591	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs210593	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs210594	0.81[ASN][1000 genomes]
rs210596	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs210601	0.85[ASN][1000 genomes]
rs210604	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs210606	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2159679	0.81[EUR][1000 genomes]
rs2533449	0.81[AFR][1000 genomes]
rs2851484	0.81[AFR][1000 genomes]
rs2851516	0.81[AFR][1000 genomes]
rs2865805	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28770244	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2903097	0.81[EUR][1000 genomes]
rs34221396	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34617709	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35696945	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4717520	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4718906	0.81[AFR][1000 genomes]
rs513150	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs532820	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs55990156	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs576293	0.82[ASN][1000 genomes]
rs585282	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs589983	0.81[ASN][1000 genomes]
rs590609	0.82[ASN][1000 genomes]
rs593063	0.82[ASN][1000 genomes]
rs595681	0.94[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.96[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs60359704	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs610930	0.94[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.96[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs6460532	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs646233	0.80[ASN][1000 genomes]
rs649200	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6943309	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6951921	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6955261	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6958981	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6961164	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6963882	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6966036	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6978134	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6979355	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6980307	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs726372	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7779010	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7786073	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7795152	0.84[ASN][1000 genomes]
rs7796973	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7797340	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7801117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7809145	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7809934	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs877687	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9332399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers 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
4	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv492242	chr7:69330737-69520566	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11974201	VKORC1L1	cis	parietal	SCAN
rs11974201	AUTS2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69311400-69371600	Weak transcription	Primary B cells from cord blood	blood
2	chr7:69326000-69335800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:69326600-69336200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:69328000-69337600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr7:69330000-69337400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:69330400-69336200	Weak transcription	Fetal Brain Male	brain
7	chr7:69330400-69337000	Weak transcription	Brain Anterior Caudate	brain
8	chr7:69330400-69338000	Weak transcription	Thymus	Thymus
9	chr7:69330600-69335600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:69330600-69337000	Weak transcription	GM12878-XiMat	blood
11	chr7:69331000-69336000	Weak transcription	Fetal Lung	lung
12	chr7:69332200-69336800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:69332400-69336600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr7:69332600-69336600	Weak transcription	Fetal Brain Female	brain
15	chr7:69332800-69336600	Weak transcription	Ovary	ovary
16	chr7:69333000-69335600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr7:69333600-69336000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:69334200-69337200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr7:69334400-69336000	Weak transcription	Dnd41	blood

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