Variant report

Variant	rs7137665
Chromosome Location	chr12:40716015-40716016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40715339..40716976-chr12:40720060..40722353,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10467144	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10735931	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10748029	0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs10748030	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10748033	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10748034	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10784486	0.80[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784501	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10784503	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10784504	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10784506	0.89[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs10784509	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10784528	0.93[YRI][hapmap]
rs10784585	0.87[CEU][hapmap]
rs10878290	0.82[ASN][1000 genomes]
rs10878358	0.90[ASN][1000 genomes]
rs10878368	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10878371	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10878377	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10878441	0.81[CHB][hapmap]
rs11176013	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1427263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427264	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1427265	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1427266	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1427267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1896252	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1896253	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1896254	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2069228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2081700	0.83[CEU][hapmap]
rs2081701	0.83[CEU][hapmap]
rs2114568	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2114569	0.85[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2162469	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2896975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4310676	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4473003	0.86[ASW][hapmap];0.93[YRI][hapmap]
rs4483664	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767969	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs4767973	0.81[JPT][hapmap]
rs4768224	0.80[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs4768227	0.85[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs4768229	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7137160	0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs715402	0.93[YRI][hapmap]
rs721709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721711	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs721712	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs721713	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7298930	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7302503	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305344	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7307276	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7307310	0.86[ASW][hapmap];0.93[YRI][hapmap]
rs7307562	0.81[CHB][hapmap];0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs7308193	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7488873	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7957057	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7963086	0.93[YRI][hapmap]
rs7979341	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs963243	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7137665	LRRK2	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
2	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
3	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:40674400-40760400	Weak transcription	Lung	lung
5	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:40684000-40722600	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:40684000-40722600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:40684000-40725000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:40695800-40723600	Weak transcription	Brain Angular Gyrus	brain
11	chr12:40699600-40721800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:40704400-40723800	Weak transcription	Brain Anterior Caudate	brain
13	chr12:40705600-40722400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:40706800-40722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:40707000-40719000	Weak transcription	A549	lung
16	chr12:40707800-40724400	Strong transcription	Primary B cells from cord blood	blood
17	chr12:40709600-40721400	Weak transcription	Ovary	ovary
18	chr12:40709800-40721600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:40709800-40722400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:40710000-40721200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:40712000-40736600	Weak transcription	Left Ventricle	heart
22	chr12:40712000-40743400	Weak transcription	Aorta	Aorta
23	chr12:40712400-40721800	Weak transcription	Adipose Nuclei	Adipose
24	chr12:40714200-40716200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:40714200-40759200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr12:40714400-40717000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr12:40715200-40718000	Strong transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links