Variant report

Variant	rs1892759
Chromosome Location	chr8:110616994-110616995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:15971362..15972270-chr8:110616217..110617145,2	MCF-7	breast:
2	chr8:110616434..110618096-chr8:110622411..110624046,2	MCF-7	breast:
3	chr8:110598326..110600037-chr8:110615498..110618470,2	K562	blood:

Variant related genes	Relation type
ENSG00000147642	Chromatin interaction
ENSG00000141027	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10088258	0.94[JPT][hapmap]
rs1009371	0.89[JPT][hapmap]
rs10108943	0.89[JPT][hapmap]
rs10111682	0.94[JPT][hapmap]
rs1013482	0.89[JPT][hapmap]
rs1026437	0.89[JPT][hapmap]
rs1044230	0.89[JPT][hapmap]
rs10505133	0.94[JPT][hapmap]
rs13439864	0.94[JPT][hapmap]
rs1379361	0.89[JPT][hapmap]
rs1379366	0.89[JPT][hapmap]
rs1379367	0.89[JPT][hapmap]
rs1457282	0.89[JPT][hapmap]
rs1457288	0.89[JPT][hapmap]
rs1457294	0.94[JPT][hapmap]
rs1457295	0.84[JPT][hapmap]
rs1563578	0.89[JPT][hapmap]
rs1563580	0.94[JPT][hapmap]
rs1617259	0.94[JPT][hapmap]
rs1630134	0.88[JPT][hapmap]
rs1630942	0.89[JPT][hapmap]
rs1673383	0.94[JPT][hapmap]
rs1673384	0.94[JPT][hapmap]
rs1673386	0.94[JPT][hapmap]
rs1673389	0.94[JPT][hapmap]
rs1673395	0.94[JPT][hapmap]
rs1673399	0.94[JPT][hapmap]
rs1673409	0.94[JPT][hapmap]
rs1673410	0.94[JPT][hapmap]
rs1673411	0.89[JPT][hapmap]
rs1673412	0.94[JPT][hapmap]
rs1673413	0.94[JPT][hapmap]
rs1673415	0.89[JPT][hapmap]
rs1673416	0.89[JPT][hapmap]
rs1673419	0.89[JPT][hapmap]
rs1673420	0.87[JPT][hapmap]
rs1673422	0.89[JPT][hapmap]
rs1673426	0.89[JPT][hapmap]
rs1673428	0.94[JPT][hapmap]
rs1783140	0.89[JPT][hapmap]
rs1783141	0.89[JPT][hapmap]
rs1783147	0.89[JPT][hapmap]
rs1783148	0.89[JPT][hapmap]
rs1783153	0.83[JPT][hapmap]
rs1783154	0.89[JPT][hapmap]
rs1783157	0.89[JPT][hapmap]
rs1783158	0.89[JPT][hapmap]
rs1783159	0.89[JPT][hapmap]
rs1783162	0.89[JPT][hapmap]
rs1783166	0.89[JPT][hapmap]
rs1783168	0.89[JPT][hapmap]
rs1783169	0.94[JPT][hapmap]
rs1783170	0.89[JPT][hapmap]
rs1783171	0.94[JPT][hapmap]
rs1783172	0.94[JPT][hapmap]
rs1783173	0.94[JPT][hapmap]
rs1783174	0.94[JPT][hapmap]
rs1892760	0.94[JPT][hapmap]
rs2022934	0.89[JPT][hapmap]
rs2022935	0.94[JPT][hapmap]
rs2154658	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2154660	0.94[JPT][hapmap]
rs2236627	1.00[JPT][hapmap]
rs2236628	0.94[JPT][hapmap]
rs2607624	0.94[JPT][hapmap]
rs2607625	0.94[JPT][hapmap]
rs2607627	0.89[JPT][hapmap]
rs2607628	0.89[JPT][hapmap]
rs2607629	0.89[JPT][hapmap]
rs2607630	0.87[JPT][hapmap]
rs2607631	0.89[JPT][hapmap]
rs2607633	0.89[JPT][hapmap]
rs2607635	0.87[JPT][hapmap]
rs2703374	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2703375	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2703377	0.82[JPT][hapmap]
rs2703380	0.81[JPT][hapmap]
rs2703382	0.94[JPT][hapmap]
rs2703384	0.94[JPT][hapmap]
rs2703386	0.89[JPT][hapmap]
rs2703388	0.94[JPT][hapmap]
rs2703389	0.89[JPT][hapmap]
rs2703390	0.91[ASN][1000 genomes]
rs2844231	0.89[JPT][hapmap]
rs2844235	0.94[JPT][hapmap]
rs2844236	0.94[JPT][hapmap]
rs2844254	0.89[JPT][hapmap]
rs2844257	0.94[JPT][hapmap]
rs2844258	0.94[JPT][hapmap]
rs2844259	0.94[JPT][hapmap]
rs2844260	0.94[JPT][hapmap]
rs2844261	0.94[JPT][hapmap]
rs3808380	0.89[JPT][hapmap]
rs4529437	0.94[JPT][hapmap]
rs7006166	0.84[JPT][hapmap]
rs7011340	0.94[JPT][hapmap]
rs7011803	0.94[JPT][hapmap]
rs730885	0.94[JPT][hapmap]
rs753995	0.89[JPT][hapmap]
rs897840	0.94[JPT][hapmap]
rs897842	0.94[JPT][hapmap]

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	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
2	esv275395	chr8:110616340-110617562	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1892759	PKHD1L1	cis	multi-tissue	Pritchard
rs1892759	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs1892759	PKHD1L1	cis	Lymphoblastoid	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110590200-110654800	Weak transcription	Lung	lung
2	chr8:110607000-110617000	Weak transcription	Hela-S3	cervix
3	chr8:110610600-110618200	Weak transcription	GM12878-XiMat	blood
4	chr8:110610600-110618600	Weak transcription	HMEC	breast
5	chr8:110611800-110617600	Enhancers	Pancreas	Pancrea
6	chr8:110612200-110624200	Weak transcription	Aorta	Aorta
7	chr8:110613000-110617400	Enhancers	HepG2	liver
8	chr8:110613600-110620800	Enhancers	Fetal Intestine Small	intestine
9	chr8:110613800-110617000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr8:110613800-110618400	Weak transcription	HUVEC	blood vessel
11	chr8:110614000-110617000	Weak transcription	A549	lung
12	chr8:110614000-110619600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr8:110614200-110618800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:110614200-110619400	Weak transcription	NHLF	lung
15	chr8:110614600-110619600	Weak transcription	Brain Substantia Nigra	brain
16	chr8:110615000-110617000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr8:110615200-110617800	Enhancers	Stomach Smooth Muscle	stomach
18	chr8:110615200-110618000	Enhancers	Colon Smooth Muscle	Colon
19	chr8:110615400-110617400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr8:110615400-110619600	Weak transcription	Esophagus	oesophagus
21	chr8:110615600-110617000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:110615600-110618000	Enhancers	Liver	Liver
23	chr8:110615600-110618600	Weak transcription	Colonic Mucosa	Colon
24	chr8:110615600-110620400	Enhancers	Duodenum Mucosa	Duodenum
25	chr8:110615600-110623000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr8:110615800-110619600	Weak transcription	Fetal Muscle Leg	muscle
27	chr8:110615800-110621600	Enhancers	Stomach Mucosa	stomach
28	chr8:110616000-110617200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr8:110616000-110619000	Weak transcription	Fetal Kidney	kidney
30	chr8:110616000-110619600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr8:110616200-110617000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr8:110616200-110617000	Weak transcription	Psoas Muscle	Psoas
33	chr8:110616200-110617200	Weak transcription	Fetal Intestine Large	intestine
34	chr8:110616200-110617200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr8:110616200-110617400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr8:110616200-110617600	Weak transcription	HSMM	muscle
37	chr8:110616200-110618800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr8:110616200-110619400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr8:110616200-110619800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr8:110616200-110620200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr8:110616200-110623000	Weak transcription	Adipose Nuclei	Adipose
42	chr8:110616400-110617200	Enhancers	Right Atrium	heart
43	chr8:110616400-110617800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr8:110616600-110617200	Enhancers	Ovary	ovary
45	chr8:110616600-110619600	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr8:110616800-110617000	Active TSS	Brain Germinal Matrix	brain
47	chr8:110616800-110617000	Enhancers	Brain Hippocampus Middle	brain
48	chr8:110616800-110617000	Active TSS	Fetal Brain Female	brain
49	chr8:110616800-110617000	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr8:110616800-110617200	Active TSS	Brain Inferior Temporal Lobe	brain

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