Variant report

Variant	rs10494583
Chromosome Location	chr1:186290495-186290496
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186286016..186287542-chr1:186289443..186290953,2	K562	blood:
2	chr1:186287759..186291220-chr1:186293517..186295510,3	K562	blood:

Variant related genes	Relation type
ENSG00000047410	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10494584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1406294	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16825150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16825183	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16825185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16825201	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16825224	0.90[ASN][1000 genomes]
rs16825230	0.88[YRI][hapmap]
rs16825243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16825248	0.90[ASN][1000 genomes]
rs16825279	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16825335	0.83[AMR][1000 genomes]
rs1919199	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1919200	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2272412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273777	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273778	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297226	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28715477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3119331	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3131554	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs34585917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736595	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3736597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3753565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766699	0.86[ASN][1000 genomes]
rs3766702	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766705	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3766707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3820181	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3820182	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.95[ASN][1000 genomes]
rs6425024	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425027	0.86[ASN][1000 genomes]
rs6425028	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs6664763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6667940	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6679066	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6689129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7514615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7525634	0.89[AMR][1000 genomes]
rs7556543	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[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	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS 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	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10494583	C1orf27	cis	cerebellum	SCAN
rs10494583	OCLM	cis	cerebellum	SCAN
rs10494583	CACNA1E	cis	cerebellum	SCAN
rs10494583	OCLM	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186272000-186306000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:186277600-186295200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:186277600-186342600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:186277800-186297000	Strong transcription	Primary B cells from cord blood	blood
5	chr1:186278400-186342600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:186278600-186292800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:186278800-186320400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:186279400-186295800	Strong transcription	A549	lung
9	chr1:186279400-186342400	Strong transcription	Fetal Thymus	thymus
10	chr1:186279600-186292200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:186279600-186317600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:186279600-186342400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:186280000-186317600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:186280000-186320200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:186280000-186340400	Strong transcription	Dnd41	blood
16	chr1:186280000-186342000	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:186280000-186342400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:186280000-186342400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr1:186280000-186342400	Strong transcription	Osteobl	bone
20	chr1:186280000-186342600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:186280000-186342600	Strong transcription	HSMM	muscle
22	chr1:186280200-186295800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:186280200-186297200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr1:186280200-186316800	Strong transcription	Placenta	Placenta
25	chr1:186280200-186342200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:186280400-186317600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:186280400-186317600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:186280400-186342400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr1:186280800-186342600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:186281000-186341800	Strong transcription	Liver	Liver
31	chr1:186281000-186342600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:186281200-186295800	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:186281200-186297400	Strong transcription	NHDF-Ad	bronchial
34	chr1:186281200-186297600	Strong transcription	Fetal Intestine Large	intestine
35	chr1:186281200-186317600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:186281200-186317800	Strong transcription	HUVEC	blood vessel
37	chr1:186281200-186338200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr1:186281200-186341400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:186281200-186341800	Strong transcription	Adipose Nuclei	Adipose
40	chr1:186281200-186342200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:186281200-186342200	Strong transcription	NH-A	brain
42	chr1:186281400-186291800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:186281400-186292400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:186281400-186295600	Strong transcription	Fetal Lung	lung
45	chr1:186281400-186297600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:186281400-186341600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:186281400-186342000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:186281400-186342000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:186281400-186342000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr1:186281400-186342200	Strong transcription	Hela-S3	cervix

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