Variant report

Variant	rs11175964
Chromosome Location	chr12:40702987-40702988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:40702957-40703026	Fibrobl	skin:	n/a	n/a

Variant related genes	Relation type
LRRK2	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10459264	0.85[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10784485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10878302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878336	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878386	0.85[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10878452	1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs11175793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175852	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175902	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175941	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11175959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176022	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11176052	0.81[JPT][hapmap]
rs11176053	0.81[JPT][hapmap]
rs11176195	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs11176261	0.85[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs11564183	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11836288	0.90[AMR][1000 genomes]
rs12314692	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12316801	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12426498	0.85[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs12426513	0.81[AMR][1000 genomes]
rs12426891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1388598	0.90[GIH][hapmap]
rs1491943	0.90[GIH][hapmap]
rs17443407	0.92[JPT][hapmap]
rs17443414	0.83[ASN][1000 genomes]
rs17490817	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17490865	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17492159	0.85[CEU][hapmap]
rs28365224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28365238	0.85[CEU][hapmap]
rs3747891	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4318033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56325408	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133914	0.85[CEU][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7308720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73101520	0.81[AMR][1000 genomes]
rs73108329	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73108339	0.90[EUR][1000 genomes]
rs73108368	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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	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

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40620800-40704200	Weak transcription	Esophagus	oesophagus
2	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
3	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
4	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
5	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:40659600-40711200	Weak transcription	Aorta	Aorta
7	chr12:40673400-40713400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:40674400-40760400	Weak transcription	Lung	lung
9	chr12:40677000-40712200	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:40680400-40709000	Weak transcription	Ovary	ovary
11	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:40684000-40722600	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:40684000-40722600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:40684000-40725000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:40690400-40709200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:40692400-40711600	Weak transcription	Adipose Nuclei	Adipose
18	chr12:40695600-40703800	Weak transcription	A549	lung
19	chr12:40695800-40723600	Weak transcription	Brain Angular Gyrus	brain
20	chr12:40697800-40703600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:40699600-40721800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:40700400-40703400	Weak transcription	Liver	Liver
23	chr12:40701200-40703600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr12:40702400-40704400	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:40702400-40706800	Strong transcription	Primary B cells from cord blood	blood
26	chr12:40702800-40703800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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