Variant report

Variant	rs1892758
Chromosome Location	chr8:110621358-110621359
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10095412	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13253969	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13254530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13254967	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16879844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1954713	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1954714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2022930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2154656	0.87[ASN][1000 genomes]
rs2703379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703381	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703383	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2703391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844243	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844248	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844249	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs34147744	0.85[ASN][1000 genomes]
rs35642643	0.84[ASN][1000 genomes]
rs4367512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61152293	0.99[ASN][1000 genomes]
rs6469270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469274	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6982034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6994349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7003380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7003744	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7813979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7825702	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656885	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1849702	chr8:110594148-110683804	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1892758	PKHD1L1	cis	multi-tissue	Pritchard
rs1892758	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs1892758	PKHD1L1	cis	Lymphoblastoid	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110590200-110654800	Weak transcription	Lung	lung
2	chr8:110612200-110624200	Weak transcription	Aorta	Aorta
3	chr8:110615600-110623000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr8:110615800-110621600	Enhancers	Stomach Mucosa	stomach
5	chr8:110616200-110623000	Weak transcription	Adipose Nuclei	Adipose
6	chr8:110617200-110625800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:110617200-110626600	Weak transcription	Right Atrium	heart
8	chr8:110617400-110632800	Weak transcription	Gastric	stomach
9	chr8:110617800-110632800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr8:110618400-110625400	Weak transcription	GM12878-XiMat	blood
11	chr8:110619800-110622600	Weak transcription	Fetal Kidney	kidney
12	chr8:110619800-110622600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr8:110619800-110622800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr8:110619800-110623000	Weak transcription	Colon Smooth Muscle	Colon
15	chr8:110619800-110623200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr8:110620000-110622200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr8:110620000-110623200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:110620200-110623800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr8:110620400-110621800	Enhancers	Brain Germinal Matrix	brain
20	chr8:110620400-110622400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:110620400-110622400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr8:110620400-110622400	Weak transcription	NHEK	skin
23	chr8:110620400-110622800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr8:110620400-110622800	Weak transcription	Fetal Muscle Leg	muscle
25	chr8:110620400-110623000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr8:110620400-110623000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr8:110620400-110623000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr8:110620400-110623000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr8:110620400-110623200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr8:110620400-110623200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr8:110620400-110623200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr8:110620400-110623200	Weak transcription	Brain Hippocampus Middle	brain
33	chr8:110620400-110626000	Weak transcription	Brain Angular Gyrus	brain
34	chr8:110620400-110631000	Weak transcription	Pancreas	Pancrea
35	chr8:110620400-110632200	Weak transcription	HMEC	breast
36	chr8:110620400-110632800	Weak transcription	Brain Substantia Nigra	brain
37	chr8:110620400-110651200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:110620400-110654800	Weak transcription	Esophagus	oesophagus
39	chr8:110620600-110621600	Enhancers	Fetal Brain Male	brain
40	chr8:110620600-110622200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:110620600-110622600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr8:110620600-110622800	Weak transcription	Hela-S3	cervix
43	chr8:110620800-110621600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr8:110620800-110622200	Weak transcription	Liver	Liver
45	chr8:110620800-110622200	Weak transcription	Fetal Intestine Small	intestine
46	chr8:110620800-110625800	Weak transcription	Brain Anterior Caudate	brain
47	chr8:110621000-110622800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr8:110621000-110625800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr8:110621200-110621600	Weak transcription	HepG2	liver
50	chr8:110621200-110622200	Weak transcription	Fetal Intestine Large	intestine

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