Variant report

Variant	rs4077987
Chromosome Location	chr12:40022029-40022030
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	chr12:40011374..40014177-chr12:40021729..40023684,2	MCF-7	breast:
2	chr12:40015362..40017426-chr12:40020461..40022505,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173208	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10047563	0.80[ASN][1000 genomes]
rs10219652	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10444570	0.91[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap]
rs10735885	0.88[JPT][hapmap]
rs10747825	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747878	0.85[JPT][hapmap]
rs10783969	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10783993	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10783994	0.82[ASN][1000 genomes]
rs10783998	0.82[ASN][1000 genomes]
rs10784001	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10784016	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10784019	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10784051	0.89[JPT][hapmap]
rs10784059	0.90[JPT][hapmap]
rs10877335	0.82[ASN][1000 genomes]
rs10877337	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10877383	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs11172998	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11173013	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11173260	0.90[CEU][hapmap]
rs11173262	0.82[AFR][1000 genomes]
rs11173440	0.91[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs11173446	0.91[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs11173459	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs11173494	1.00[ASW][hapmap];0.83[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs11173507	0.91[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11173541	0.90[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs11173550	0.90[JPT][hapmap]
rs12229203	0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.87[YRI][hapmap]
rs12229301	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12229418	0.91[CEU][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap]
rs12230687	0.91[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12823801	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12825223	0.82[AFR][1000 genomes]
rs4129365	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap]
rs4238072	0.90[JPT][hapmap]
rs4238073	0.86[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap]
rs4312128	0.90[JPT][hapmap];0.87[YRI][hapmap]
rs4337105	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4357762	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4405390	0.89[JPT][hapmap]
rs4411336	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4417381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4417382	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4495951	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs4594067	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4767949	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4768166	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs4768168	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4768169	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs61933102	0.82[ASN][1000 genomes]
rs6421191	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6421195	0.82[ASN][1000 genomes]
rs6421196	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[ASN][1000 genomes]
rs6421197	0.82[ASN][1000 genomes]
rs6421198	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6581250	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6581263	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6581265	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6581266	0.82[ASN][1000 genomes]
rs6581270	0.82[CEU][hapmap];0.93[GIH][hapmap];0.82[ASN][1000 genomes]
rs6581271	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs6581272	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7136929	0.82[ASN][1000 genomes]
rs7296585	0.91[CEU][hapmap];0.82[ASN][1000 genomes]
rs7485345	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7486196	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7486621	0.82[ASN][1000 genomes]
rs7486631	0.83[CHB][hapmap];0.85[YRI][hapmap]
rs7487999	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7952735	0.82[ASN][1000 genomes]
rs7956577	0.82[ASN][1000 genomes]
rs7959905	0.81[ASN][1000 genomes]
rs7961070	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7961346	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7973312	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7980636	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9325166	0.83[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]

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	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1039645	chr12:39903123-40022029	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv469359	chr12:39946354-40034699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv558591	chr12:39946354-40034699	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv469361	chr12:39946354-40042220	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv558592	chr12:39946354-40042220	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv899014	chr12:39946354-40068896	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv899015	chr12:39946354-40118249	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv899017	chr12:39949147-40081619	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv899018	chr12:39949147-40111761	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv899020	chr12:39985206-40040331	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv899021	chr12:39989172-40053423	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv899022	chr12:40014427-40111761	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4077987	LRRK2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40018000-40022400	Weak transcription	GM12878-XiMat	blood
2	chr12:40019600-40024800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr12:40020000-40024600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr12:40020200-40022800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr12:40020200-40024400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:40020400-40024400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr12:40020600-40022800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:40020800-40022600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr12:40021200-40022600	Enhancers	Primary T cells from cord blood	blood
10	chr12:40021200-40024400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:40021400-40023000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:40021600-40022200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr12:40021600-40022800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr12:40021600-40022800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr12:40021600-40022800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:40021600-40023600	Enhancers	Dnd41	blood
17	chr12:40022000-40036800	Weak transcription	K562	blood

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