Variant report

Variant	rs10489276
Chromosome Location	chr1:172862939-172862940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172861260..172863626-chr1:172948311..172950341,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10912488	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10912490	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10912491	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12021711	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12025176	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12037853	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12047983	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12136659	0.84[EUR][1000 genomes]
rs12403628	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12411259	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12728265	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12739009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12747422	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12748081	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2157453	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157454	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187892	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213742	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213745	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2422257	1.00[JPT][hapmap]
rs35715673	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4145468	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4145469	1.00[JPT][hapmap]
rs4916198	0.87[EUR][1000 genomes]
rs4916283	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916285	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55724017	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6425143	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6425145	0.94[EUR][1000 genomes]
rs6425146	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6661686	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6672776	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6688532	1.00[JPT][hapmap]
rs6699678	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68143871	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7517810	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7527462	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527986	1.00[JPT][hapmap]
rs7539319	1.00[JPT][hapmap]
rs9286879	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv3587	chr1:172836950-172882218	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489276	ANKRD45	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172861800-172863000	Enhancers	Left Ventricle	heart
2	chr1:172861800-172863000	Flanking Active TSS	Hela-S3	cervix
3	chr1:172861800-172863200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr1:172862000-172863200	Enhancers	Psoas Muscle	Psoas
5	chr1:172862000-172864000	Enhancers	A549	lung
6	chr1:172862000-172864200	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr1:172862200-172863000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:172862200-172863200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:172862200-172863800	Enhancers	Dnd41	blood
10	chr1:172862200-172864400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:172862400-172863000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:172862400-172863000	Enhancers	Pancreas	Pancrea
13	chr1:172862400-172863000	Enhancers	Osteobl	bone
14	chr1:172862400-172863200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:172862400-172863200	Enhancers	Stomach Mucosa	stomach
16	chr1:172862400-172863600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:172862400-172863800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:172862400-172863800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr1:172862400-172863800	Enhancers	GM12878-XiMat	blood
20	chr1:172862400-172863800	Enhancers	NHEK	skin
21	chr1:172862600-172863000	Flanking Active TSS	HUVEC	blood vessel
22	chr1:172862600-172863200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr1:172862600-172863600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:172862600-172863800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:172862600-172863800	Weak transcription	Adipose Nuclei	Adipose
26	chr1:172862600-172865200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:172862800-172863000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:172862800-172863000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr1:172862800-172863000	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr1:172862800-172863000	Enhancers	Small Intestine	intestine
31	chr1:172862800-172863000	Enhancers	NHDF-Ad	bronchial
32	chr1:172862800-172863400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:172862800-172863600	Weak transcription	NHLF	lung
34	chr1:172862800-172863800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:172862800-172863800	Weak transcription	Fetal Thymus	thymus
36	chr1:172862800-172864000	Weak transcription	HSMM	muscle
37	chr1:172862800-172864200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:172862800-172864200	Weak transcription	Ovary	ovary
39	chr1:172862800-172864400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:172862800-172864400	Weak transcription	NH-A	brain
41	chr1:172862800-172866800	Weak transcription	HMEC	breast

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