Variant report

Variant	rs9472413
Chromosome Location	chr6:44945717-44945718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10080909	0.84[EUR][1000 genomes]
rs10498757	1.00[ASN][1000 genomes]
rs13436998	0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs16872751	1.00[CHB][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16873056	0.82[CEU][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873073	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873103	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873150	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17209608	0.82[CEU][hapmap]
rs2090832	1.00[CHB][hapmap]
rs2396374	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28843161	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59606274	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6912535	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6925770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73438898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73442933	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73443219	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73443229	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73443286	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73444394	1.00[ASN][1000 genomes]
rs73444966	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73444983	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73447073	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73447433	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73448343	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73451303	0.83[EUR][1000 genomes]
rs7742332	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7749796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751298	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7766901	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7768241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296447	0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9296450	0.83[MKK][hapmap];1.00[YRI][hapmap]
rs9296451	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs9463046	1.00[CHB][hapmap];0.88[MKK][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9463053	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9463056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs9463071	0.83[EUR][1000 genomes]
rs9472371	1.00[CHB][hapmap]
rs9472372	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472373	1.00[CHB][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472374	1.00[CHB][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472375	1.00[CHB][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472377	1.00[CHB][hapmap]
rs9472379	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472381	1.00[CHB][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472384	1.00[CHB][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472390	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472391	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472393	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472395	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472412	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472414	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9472421	1.00[CEU][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472424	1.00[ASN][1000 genomes]
rs9472427	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9472433	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs9472434	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs9472435	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472436	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472438	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9885623	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885861	chr6:44837356-45043618	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	esv2758051	chr6:44879791-45056758	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2759423	chr6:44879791-45056758	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv885862	chr6:44890760-45083966	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv885863	chr6:44890760-45083966	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv462938	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv470817	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv603007	chr6:44909515-45008779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1023018	chr6:44925393-45152912	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv538212	chr6:44925393-45152912	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv970117	chr6:44945572-44946769	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9472413	KIAA0240	cis	parietal	SCAN
rs9472413	TAF8	cis	cerebellum	SCAN
rs9472413	GUCA1B	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44939800-44951200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:44940800-44957000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:44941600-44947000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr6:44942200-44946400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr6:44942200-44947000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr6:44942400-44946600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:44942400-44946800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:44942800-44946800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:44943000-44947000	Weak transcription	Fetal Heart	heart
10	chr6:44943400-44946600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr6:44943400-44946600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr6:44943400-44946600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:44943600-44946000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr6:44943800-44946200	Enhancers	Dnd41	blood
15	chr6:44945000-44946600	Enhancers	Primary T cells from cord blood	blood
16	chr6:44945200-44946000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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