Variant report

Variant	rs3863401
Chromosome Location	chr15:99881220-99881221
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1033035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1033036	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs10902543	0.85[JPT][hapmap]
rs10902544	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11247079	0.84[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11247081	0.98[ASN][1000 genomes]
rs11853278	0.85[CEU][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12911768	0.91[YRI][hapmap]
rs12912927	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1472989	0.98[ASN][1000 genomes]
rs1876927	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2048305	0.85[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2089707	0.87[JPT][hapmap]
rs2175225	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2202941	0.81[AMR][1000 genomes]
rs28520505	0.94[ASN][1000 genomes]
rs2862139	0.96[YRI][hapmap]
rs28807370	0.84[MEX][hapmap]
rs3851679	0.99[ASN][1000 genomes]
rs4965474	0.87[JPT][hapmap]
rs58946939	0.88[ASN][1000 genomes]
rs6598237	0.82[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7167119	0.85[CEU][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7167542	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7167899	0.92[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7168227	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7169906	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7171970	0.95[ASN][1000 genomes]
rs7173844	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7182425	0.90[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs7498053	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8036160	0.89[GIH][hapmap];0.91[JPT][hapmap]
rs8040850	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs8041923	0.85[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs8042021	0.81[YRI][hapmap]
rs8042249	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs8042667	0.89[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
16	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
17	nsv1052683	chr15:99869631-99924685	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
18	nsv542521	chr15:99869631-99924685	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3863401	C15orf51	cis	cerebellum	SCAN
rs3863401	LRRK1	cis	cerebellum	SCAN
rs3863401	TTC23	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99859400-99906600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:99863200-99899800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:99864400-99902200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:99864800-99881400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:99864800-99884200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr15:99866800-99882400	Weak transcription	Gastric	stomach
7	chr15:99867200-99926600	Weak transcription	NHEK	skin
8	chr15:99869200-99882000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:99869600-99893400	Weak transcription	Aorta	Aorta
10	chr15:99869800-99884600	Weak transcription	GM12878-XiMat	blood
11	chr15:99870200-99884400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:99870200-99884600	Weak transcription	Primary B cells from cord blood	blood
13	chr15:99871200-99893000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:99871400-99888200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:99871600-99895200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:99872000-99893200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:99872000-99906600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:99872000-99912600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:99872600-99909000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:99872800-99906200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:99872800-99911400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:99873200-99884000	Weak transcription	Right Atrium	heart
23	chr15:99873200-99894800	Weak transcription	Brain Angular Gyrus	brain
24	chr15:99873400-99886200	Weak transcription	Esophagus	oesophagus
25	chr15:99874200-99893200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr15:99874400-99881400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:99874400-99887600	Weak transcription	Spleen	Spleen
28	chr15:99874400-99893200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:99874400-99893400	Weak transcription	Lung	lung
30	chr15:99874400-99903400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:99874600-99895400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr15:99874600-99906600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr15:99875800-99882000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:99875800-99883200	Weak transcription	Brain Germinal Matrix	brain
35	chr15:99876200-99881400	Weak transcription	Placenta	Placenta
36	chr15:99876200-99884000	Weak transcription	Left Ventricle	heart
37	chr15:99876200-99893200	Weak transcription	Pancreas	Pancrea
38	chr15:99876200-99902200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:99877000-99888600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:99877000-99893400	Weak transcription	Adipose Nuclei	Adipose
41	chr15:99877400-99884200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:99877600-99882000	Weak transcription	Dnd41	blood
43	chr15:99877600-99885200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:99877600-99893200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr15:99877800-99882000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:99877800-99906200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:99878000-99901600	Weak transcription	Thymus	Thymus
48	chr15:99878200-99882200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:99878200-99893000	Weak transcription	Fetal Thymus	thymus
50	chr15:99878200-99906600	Weak transcription	Fetal Muscle Trunk	muscle

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