Variant report

Variant	rs189798
Chromosome Location	chr8:8990577-8990578
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	chr8:8986821..8989144-chr8:8989277..8990875,2	MCF-7	breast:
2	chr8:8983449..8987686-chr8:8988360..8992569,4	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10089635	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12785	0.88[EUR][1000 genomes]
rs330903	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs330904	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs330905	0.85[EUR][1000 genomes]
rs330908	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs330909	0.88[EUR][1000 genomes]
rs330910	0.85[EUR][1000 genomes]
rs330911	0.82[EUR][1000 genomes]
rs330912	0.88[EUR][1000 genomes]
rs330915	0.80[EUR][1000 genomes]
rs330916	0.81[EUR][1000 genomes]
rs330917	0.81[EUR][1000 genomes]
rs330919	0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs330920	0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs330921	0.93[TSI][hapmap]
rs330922	0.86[EUR][1000 genomes]
rs330923	0.86[EUR][1000 genomes]
rs9949	0.92[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1022328	chr8:8954003-9061281	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv610206	chr8:8961017-9162048	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1026279	chr8:8982622-9030279	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Myopia (pathological)	23049088	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs189798	FLJ10661	cis	cerebellum	SCAN
rs189798	DEFB134	cis	cerebellum	SCAN
rs189798	PRSS55	cis	cerebellum	SCAN
rs189798	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs189798	DEFB136	cis	parietal	SCAN
rs189798	RP1L1	cis	cerebellum	SCAN
rs189798	PPP1R3B	cis	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8962000-8991400	Weak transcription	Psoas Muscle	Psoas
2	chr8:8974600-8991600	Weak transcription	Aorta	Aorta
3	chr8:8983800-8992000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:8984400-8991400	Weak transcription	NHEK	skin
5	chr8:8986000-8993000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr8:8987800-8997400	Weak transcription	Spleen	Spleen
7	chr8:8988600-8990800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr8:8989200-8992600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr8:8989200-8992800	Enhancers	Fetal Heart	heart
10	chr8:8989200-8997400	Weak transcription	Gastric	stomach
11	chr8:8989400-8991200	Weak transcription	Right Ventricle	heart
12	chr8:8989400-8991400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr8:8989400-8992000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr8:8989400-8992200	Weak transcription	Fetal Stomach	stomach
15	chr8:8989400-8992400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr8:8989400-8992600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr8:8989400-8993000	Enhancers	Left Ventricle	heart
18	chr8:8989400-8993600	Weak transcription	K562	blood
19	chr8:8989600-8996800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr8:8989800-8992400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr8:8990000-8990600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr8:8990000-8992400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr8:8990000-8993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr8:8990000-8993200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr8:8990000-8993400	Enhancers	Placenta	Placenta
26	chr8:8990200-8990600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr8:8990200-8990800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr8:8990200-8991000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr8:8990200-8992600	Enhancers	Adipose Nuclei	Adipose
30	chr8:8990200-8992600	Enhancers	HUVEC	blood vessel
31	chr8:8990200-8992600	Enhancers	Osteobl	bone
32	chr8:8990200-8993000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr8:8990200-8993000	Enhancers	Right Atrium	heart
34	chr8:8990200-8995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr8:8990400-8991200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr8:8990400-8991400	Weak transcription	Fetal Muscle Leg	muscle
37	chr8:8990400-8992600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr8:8990400-8994800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr8:8990400-8997600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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