Variant report

Variant	rs1870389
Chromosome Location	chr8:110351254-110351255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:110344786..110348564-chr8:110349076..110353866,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120526	Chromatin interaction
ENSG00000120533	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11998321	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13439864	0.82[CEU][hapmap]
rs1673409	0.84[MEX][hapmap]
rs1673412	0.80[MEX][hapmap]
rs1783169	0.80[MEX][hapmap]
rs2022935	0.80[MEX][hapmap]
rs2926229	0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926230	0.81[ASN][1000 genomes]
rs2926232	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926233	0.94[CHB][hapmap];0.90[JPT][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926234	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926237	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2926239	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2926242	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980570	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980586	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891273	chr8:110219735-110475874	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv891279	chr8:110268104-110450092	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv891280	chr8:110346363-110465481	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1870389	PKHD1L1	cis	multi-tissue	Pritchard
rs1870389	PKHD1L1	cis	lymphoblastoid	seeQTL
rs1870389	PKHD1L1	cis	Lymphoblastoid	GTEx
rs1870389	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110347000-110358200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:110347000-110358400	Weak transcription	Spleen	Spleen
3	chr8:110347000-110358800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:110347200-110354800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:110347200-110355000	Weak transcription	Lung	lung
6	chr8:110347200-110357600	Weak transcription	Pancreas	Pancrea
7	chr8:110347200-110358200	Weak transcription	Esophagus	oesophagus
8	chr8:110347200-110359800	Weak transcription	Gastric	stomach
9	chr8:110347400-110356200	Weak transcription	Ovary	ovary
10	chr8:110347400-110358000	Weak transcription	Colonic Mucosa	Colon
11	chr8:110347400-110358400	Weak transcription	Fetal Brain Male	brain
12	chr8:110347400-110359400	Weak transcription	Aorta	Aorta
13	chr8:110347400-110359400	Weak transcription	Brain Substantia Nigra	brain
14	chr8:110347400-110360000	Weak transcription	Stomach Mucosa	stomach
15	chr8:110347600-110354800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr8:110347600-110354800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr8:110347600-110356000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr8:110347600-110357800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:110347600-110358200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr8:110347600-110358200	Weak transcription	HSMMtube	muscle
21	chr8:110347600-110358400	Weak transcription	Fetal Stomach	stomach
22	chr8:110348000-110356200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr8:110348000-110358400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr8:110348200-110353400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr8:110348200-110355200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr8:110348200-110356600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr8:110348200-110356600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr8:110348200-110356600	Strong transcription	A549	lung
29	chr8:110348200-110356800	Strong transcription	Placenta	Placenta
30	chr8:110348200-110356800	Strong transcription	NH-A	brain
31	chr8:110348200-110357000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr8:110348200-110357000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr8:110348200-110357400	Strong transcription	Primary B cells from cord blood	blood
34	chr8:110348200-110357400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr8:110348200-110357400	Strong transcription	Fetal Intestine Large	intestine
36	chr8:110348400-110353000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr8:110348400-110354000	Weak transcription	Brain Germinal Matrix	brain
38	chr8:110348400-110356200	Weak transcription	Fetal Muscle Leg	muscle
39	chr8:110348400-110356400	Weak transcription	Right Ventricle	heart
40	chr8:110348400-110356600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr8:110348400-110357000	Strong transcription	HSMM	muscle
42	chr8:110348400-110360200	Weak transcription	Fetal Intestine Small	intestine
43	chr8:110348600-110356600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr8:110348600-110357400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr8:110348600-110357400	Strong transcription	Fetal Thymus	thymus
46	chr8:110348600-110358200	Weak transcription	NHEK	skin
47	chr8:110348800-110351800	Weak transcription	Hela-S3	cervix
48	chr8:110348800-110353400	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr8:110348800-110353400	Strong transcription	NHLF	lung
50	chr8:110348800-110357000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links