Variant report

Variant	rs4651330
Chromosome Location	chr1:186816650-186816651
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10489407	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10732978	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10737270	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10752977	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10752978	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10752979	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10798060	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798061	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10911933	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911934	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10911937	0.95[JPT][hapmap]
rs2205897	0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4651331	0.90[JPT][hapmap]
rs4651334	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6425051	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425052	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6425053	0.82[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6669230	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682761	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685652	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6687896	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6688584	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7521601	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7522183	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532616	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7541946	0.85[EUR][1000 genomes];0.92[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	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4651330	C1orf25	cis	parietal	SCAN
rs4651330	OCLM	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186800200-186827800	Weak transcription	NHEK	skin
2	chr1:186801000-186818400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:186808600-186828200	Weak transcription	Pancreas	Pancrea
4	chr1:186808600-186830800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:186810400-186824800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:186812200-186817400	Weak transcription	Fetal Intestine Large	intestine
7	chr1:186812200-186817400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:186813000-186817000	Weak transcription	Small Intestine	intestine
9	chr1:186815200-186816800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:186815200-186816800	Weak transcription	A549	lung
11	chr1:186815200-186823400	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:186815200-186844800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:186815400-186816800	Weak transcription	Adipose Nuclei	Adipose
14	chr1:186815400-186816800	Weak transcription	Fetal Intestine Small	intestine
15	chr1:186815400-186816800	Weak transcription	Stomach Mucosa	stomach
16	chr1:186815400-186817200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:186815400-186817200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:186815400-186817400	Weak transcription	GM12878-XiMat	blood
19	chr1:186815400-186818600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:186815400-186818800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:186815600-186816800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr1:186815600-186817000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:186815800-186816800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:186815800-186817200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:186815800-186817800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:186816200-186820000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:186816400-186817200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:186816400-186818000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:186816600-186817200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:186816600-186817400	Strong transcription	Hela-S3	cervix
31	chr1:186816600-186818000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:186816600-186818400	Enhancers	Brain Hippocampus Middle	brain

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