Variant report

Variant	rs4768224
Chromosome Location	chr12:40661403-40661404
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10467144	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs10735931	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10748029	0.85[ASN][1000 genomes]
rs10748030	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10748033	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10748034	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784486	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784501	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784503	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784504	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784506	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784509	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs10784585	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs10878290	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10878358	0.85[ASN][1000 genomes]
rs10878368	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs10878371	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs10878377	0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11176013	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs1427263	0.80[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs1427264	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs1427265	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs1427266	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs1427267	0.80[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs1896252	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs1896253	0.87[CHB][hapmap]
rs1896254	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs2069228	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2081700	0.82[CEU][hapmap]
rs2081701	0.82[CEU][hapmap]
rs2114568	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs2114569	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs2162469	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs2896975	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4310676	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4473003	0.81[ASW][hapmap]
rs4483664	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767969	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs4768227	0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs4768229	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs7137160	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs7137665	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]
rs721709	0.80[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs721711	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs721712	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs721713	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs7298930	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs7302503	0.80[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7305344	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7307276	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs7307310	0.81[ASW][hapmap]
rs7307562	0.84[CHD][hapmap]
rs7308193	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488873	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957057	0.93[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973479	0.82[CHB][hapmap]
rs7979341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs963243	0.83[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1045408	chr12:40620554-40664424	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
3	nsv1042967	chr12:40629636-40710319	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4768224	LRRK2	cis	parietal	SCAN
rs4768224	KIF21A	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart
2	chr12:40620800-40704200	Weak transcription	Esophagus	oesophagus
3	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
4	chr12:40630600-40669400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:40630600-40686400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:40640200-40680400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
8	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
9	chr12:40641200-40662800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:40642200-40682400	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:40647600-40674000	Weak transcription	Lung	lung
12	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr12:40659400-40677800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:40659400-40678600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:40659400-40678600	Weak transcription	Ovary	ovary
16	chr12:40659400-40682200	Weak transcription	Brain Anterior Caudate	brain
17	chr12:40659400-40686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:40659600-40669600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:40659600-40670000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:40659600-40670000	Weak transcription	Adipose Nuclei	Adipose
21	chr12:40659600-40670000	Weak transcription	Liver	Liver
22	chr12:40659600-40677000	Weak transcription	A549	lung
23	chr12:40659600-40680000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:40659600-40680200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:40659600-40694600	Weak transcription	Psoas Muscle	Psoas
26	chr12:40659600-40711200	Weak transcription	Aorta	Aorta
27	chr12:40660600-40671600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:40661000-40661600	Enhancers	Colon Smooth Muscle	Colon
29	chr12:40661000-40661800	Strong transcription	Primary B cells from cord blood	blood
30	chr12:40661000-40683400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr12:40661200-40661600	Enhancers	Rectal Smooth Muscle	rectum

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