Variant report

Variant	rs1045529
Chromosome Location	chr8:8890098-8890099
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	chr8:8866297..8868833-chr8:8887524..8890339,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1045527	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs11784393	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11785819	0.89[CEU][hapmap]
rs11787026	0.82[CEU][hapmap]
rs12114954	0.82[CEU][hapmap]
rs13252797	0.89[CEU][hapmap]
rs13271797	0.89[CEU][hapmap]
rs13272451	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1562211	0.91[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2044387	0.84[CHB][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2044388	0.85[CHB][hapmap]
rs2288671	0.96[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.85[EUR][1000 genomes]
rs2288673	0.85[EUR][1000 genomes]
rs2915251	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs2915252	0.95[CHD][hapmap]
rs2921378	0.89[AMR][1000 genomes]
rs2921383	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2953805	0.88[AMR][1000 genomes]
rs2953806	0.92[AMR][1000 genomes]
rs2956242	0.95[CHD][hapmap]
rs2956243	0.95[CHD][hapmap]
rs2956244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2979246	0.82[CHD][hapmap]
rs2979247	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2979253	0.95[AMR][1000 genomes]
rs2979256	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2979265	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs3021416	0.92[AMR][1000 genomes]
rs4537305	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4841083	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4841084	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4841085	0.94[JPT][hapmap]
rs6601280	0.85[CEU][hapmap]
rs6748	0.89[CEU][hapmap];0.80[TSI][hapmap]
rs6983877	0.82[CEU][hapmap]
rs6987558	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6993244	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7005133	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7016139	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7017868	0.89[CEU][hapmap]
rs7813388	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs7824140	0.86[ASN][1000 genomes]
rs7839585	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs7853	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9329175	0.85[CEU][hapmap]
rs9650616	0.89[CEU][hapmap]

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	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	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
3	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv610205	chr8:8799111-8891644	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	n/a
5	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
6	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
7	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

Variant related diseases (count:1)

Disease	PMID	Source
Myopia (pathological)	23049088	GWAS catalog

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs1045529	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs1045529	CLDN23	cis	multi-tissue	Pritchard
rs1045529	CTSB	cis	cerebellum	SCAN
rs1045529	RP11-10A14.5	cis	Whole Blood	GTEx
rs1045529	PRSS55	cis	cerebellum	SCAN
rs1045529	FLJ10661	cis	cerebellum	SCAN
rs1045529	C8orf13	cis	multi-tissue	Pritchard
rs1045529	RP11-62H7.2	cis	Stomach	GTEx
rs1045529	THEX1	Cis_1M	lymphoblastoid	RTeQTL
rs1045529	RP11-62H7.2	cis	Thyroid	GTEx
rs1045529	TDH	cis	cerebellum	SCAN
rs1045529	MFHAS1	cis	cerebellum	SCAN
rs1045529	SGK223	cis	Thyroid	GTEx
rs1045529	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs1045529	PPP1R3B	cis	cerebellum	SCAN
rs1045529	DEFB134	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8861200-8892400	Weak transcription	Aorta	Aorta
2	chr8:8861400-8907000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:8861800-8891400	Weak transcription	Brain Angular Gyrus	brain
4	chr8:8861800-8891800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr8:8861800-8892000	Weak transcription	Brain Anterior Caudate	brain
6	chr8:8861800-8892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:8861800-8892200	Weak transcription	Ovary	ovary
8	chr8:8861800-8893800	Weak transcription	Fetal Brain Male	brain
9	chr8:8861800-8897800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr8:8861800-8915600	Weak transcription	Pancreas	Pancrea
11	chr8:8870600-8892200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr8:8871200-8900000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr8:8871400-8892800	Weak transcription	HSMMtube	muscle
14	chr8:8871800-8894400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr8:8872000-8891200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr8:8875000-8891200	Weak transcription	Fetal Intestine Small	intestine
17	chr8:8875200-8897200	Weak transcription	Gastric	stomach
18	chr8:8875400-8890200	Weak transcription	Fetal Stomach	stomach
19	chr8:8875400-8892600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr8:8875400-8894400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr8:8875400-8897000	Weak transcription	Lung	lung
22	chr8:8875400-8901200	Weak transcription	Thymus	Thymus
23	chr8:8875600-8890200	Weak transcription	HSMM	muscle
24	chr8:8875800-8892200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr8:8876400-8898000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr8:8876800-8891400	Weak transcription	Fetal Brain Female	brain
27	chr8:8877000-8894600	Weak transcription	HMEC	breast
28	chr8:8877000-8895600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr8:8877000-8903400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr8:8877200-8895400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr8:8878600-8890200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr8:8878800-8890200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr8:8879200-8892600	Weak transcription	Osteobl	bone
34	chr8:8879400-8894200	Weak transcription	HepG2	liver
35	chr8:8880600-8890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr8:8881000-8900400	Weak transcription	NH-A	brain
37	chr8:8881200-8892000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr8:8881600-8891400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr8:8882200-8896400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr8:8882600-8894600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr8:8882600-8894600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr8:8883000-8893200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr8:8883200-8898400	Weak transcription	Fetal Kidney	kidney
44	chr8:8883600-8902400	Weak transcription	Adipose Nuclei	Adipose
45	chr8:8883800-8891000	Weak transcription	Stomach Mucosa	stomach
46	chr8:8883800-8892200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr8:8883800-8893800	Weak transcription	NHDF-Ad	bronchial
48	chr8:8883800-8895400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr8:8883800-8897800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr8:8883800-8906000	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links