Variant report

Variant	rs12592075
Chromosome Location	chr15:99836804-99836805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1033036	0.81[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10794475	0.86[YRI][hapmap]
rs10902543	0.90[JPT][hapmap];0.96[YRI][hapmap]
rs10902544	0.84[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11247074	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11247075	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11247079	0.89[ASW][hapmap];0.84[CEU][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11247080	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11247081	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11853278	0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11853850	0.82[YRI][hapmap]
rs12438814	0.82[ASN][1000 genomes]
rs12592452	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904429	0.82[ASN][1000 genomes]
rs12906357	0.89[YRI][hapmap]
rs12913897	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];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1472988	0.82[ASN][1000 genomes]
rs1472989	0.82[AMR][1000 genomes]
rs1812344	0.84[AFR][1000 genomes]
rs1876927	0.84[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2048305	0.81[GIH][hapmap]
rs2089707	0.91[JPT][hapmap]
rs28520505	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs28696045	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4965225	0.86[YRI][hapmap]
rs4965474	0.91[JPT][hapmap]
rs58946939	0.82[AMR][1000 genomes]
rs6598237	0.83[ASW][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7162949	0.86[YRI][hapmap]
rs7167119	0.91[JPT][hapmap];0.82[AMR][1000 genomes]
rs7167899	0.87[JPT][hapmap]
rs7168227	0.89[ASW][hapmap];0.84[CEU][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs7169906	0.81[JPT][hapmap];0.96[YRI][hapmap]
rs7181739	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7182425	0.83[ASW][hapmap];0.84[CEU][hapmap];0.89[GIH][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7182675	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8036160	0.84[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap]
rs8040850	0.80[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs8041923	0.94[ASW][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8042249	0.84[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs8042667	0.89[ASW][hapmap];0.84[CEU][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
13	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
15	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats 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 miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12592075	C15orf51	cis	cerebellum	SCAN
rs12592075	LRRK1	cis	cerebellum	SCAN
rs12592075	LRRK1	cis	parietal	SCAN
rs12592075	TTC23	cis	lymphoblastoid	seeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99792200-99846400	Weak transcription	Lung	lung
2	chr15:99792800-99847000	Weak transcription	Right Ventricle	heart
3	chr15:99793000-99838000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:99793000-99850400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:99793000-99866600	Weak transcription	Gastric	stomach
6	chr15:99794000-99840000	Weak transcription	Brain Anterior Caudate	brain
7	chr15:99794000-99846400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:99794200-99847000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:99794400-99845200	Weak transcription	HSMMtube	muscle
10	chr15:99798000-99838200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr15:99799400-99838200	Weak transcription	Fetal Lung	lung
12	chr15:99808800-99845200	Weak transcription	Fetal Kidney	kidney
13	chr15:99809000-99846400	Weak transcription	Pancreas	Pancrea
14	chr15:99809000-99846400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:99814200-99838400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:99816400-99838800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:99816800-99846400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:99817000-99845000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:99819600-99838200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:99819800-99854800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:99823000-99838200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:99823000-99841800	Weak transcription	Small Intestine	intestine
23	chr15:99823000-99846200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:99824000-99847000	Weak transcription	Spleen	Spleen
25	chr15:99824400-99837000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:99824400-99838200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:99824400-99845600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr15:99824600-99838200	Weak transcription	NHDF-Ad	bronchial
29	chr15:99824800-99846200	Weak transcription	Fetal Brain Female	brain
30	chr15:99825000-99841000	Weak transcription	Fetal Heart	heart
31	chr15:99825200-99838400	Weak transcription	Esophagus	oesophagus
32	chr15:99825200-99843400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:99827200-99846000	Weak transcription	NHEK	skin
34	chr15:99827800-99845200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:99827800-99846400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:99828400-99838400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:99829600-99847000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:99829800-99846400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:99831400-99848800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:99832000-99837200	Strong transcription	Primary T cells from cord blood	blood
41	chr15:99832400-99838400	Weak transcription	Aorta	Aorta
42	chr15:99832600-99838200	Weak transcription	Adipose Nuclei	Adipose
43	chr15:99832600-99838200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:99832600-99846800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:99833000-99844200	Weak transcription	Fetal Stomach	stomach
46	chr15:99833200-99875800	Weak transcription	Thymus	Thymus
47	chr15:99833400-99841600	Weak transcription	Brain Hippocampus Middle	brain
48	chr15:99833600-99840000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:99834200-99851800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:99834600-99838200	Weak transcription	Fetal Muscle Trunk	muscle

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