Variant report

Variant	rs10489385
Chromosome Location	chr1:210572437-210572438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:210544698..210555948-chr1:210566953..210584306,65	MCF-7	breast:
2	chr1:210572425..210575594-chr1:210579116..210581300,3	K562	blood:
3	chr1:210544801..210552702-chr1:210569747..210575327,18	MCF-7	breast:
4	chr1:210565121..210568359-chr1:210572172..210574144,3	K562	blood:
5	chr1:210551526..210553574-chr1:210572140..210575060,2	K562	blood:
6	chr1:210546689..210549252-chr1:210570902..210574338,5	K562	blood:
7	chr1:210547526..210548278-chr1:210571817..210572528,2	MCF-7	breast:
8	chr1:210570801..210572444-chr1:210574619..210577549,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1005174	1.00[AFR][1000 genomes]
rs10489383	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10489386	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10863819	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs10863820	1.00[AFR][1000 genomes]
rs10863822	0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10863825	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119458	1.00[AFR][1000 genomes]
rs11119462	1.00[AFR][1000 genomes]
rs11119473	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11119475	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11119485	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12024862	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12030512	0.86[AFR][1000 genomes]
rs12030856	0.86[AFR][1000 genomes]
rs12034871	0.86[AFR][1000 genomes]
rs12040684	0.86[AFR][1000 genomes]
rs12046133	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12049137	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12062126	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12087955	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12120970	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12134251	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12138216	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs12141780	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12143463	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12143703	1.00[ASW][hapmap]
rs12145163	1.00[ASW][hapmap]
rs1338289	1.00[ASW][hapmap];0.82[CHD][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs17016002	0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17260438	1.00[ASW][hapmap]
rs2143591	1.00[AFR][1000 genomes]
rs2294843	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2294851	1.00[ASW][hapmap];0.85[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2357584	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3753230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3765856	0.82[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3765865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3765866	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3765877	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3765878	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3765886	1.00[AFR][1000 genomes]
rs3819985	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs4844520	1.00[AFR][1000 genomes]
rs4844996	0.86[AFR][1000 genomes]
rs4844997	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs58469250	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs58960429	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs60154123	0.86[AFR][1000 genomes]
rs628908	1.00[MKK][hapmap]
rs650728	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs701943	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs701944	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs7525927	1.00[AFR][1000 genomes]
rs7550576	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs845452	1.00[ASW][hapmap]
rs845455	1.00[ASW][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10489385	SYT14	cis	parietal	SCAN
rs10489385	DYRK3	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210529600-210586000	Weak transcription	Pancreas	Pancrea
2	chr1:210551400-210586000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:210559000-210584400	Weak transcription	Fetal Stomach	stomach
4	chr1:210566800-210586200	Weak transcription	Lung	lung
5	chr1:210567400-210617200	Weak transcription	Left Ventricle	heart
6	chr1:210568200-210572600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:210568200-210573800	Weak transcription	Aorta	Aorta
8	chr1:210568800-210573800	Weak transcription	Osteobl	bone
9	chr1:210569200-210573600	Weak transcription	HepG2	liver
10	chr1:210569400-210573600	Weak transcription	Right Ventricle	heart
11	chr1:210570200-210573400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:210570200-210594000	Weak transcription	Fetal Lung	lung
13	chr1:210570400-210574400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:210571200-210573200	Weak transcription	GM12878-XiMat	blood
15	chr1:210571200-210573800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:210571200-210573800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:210571200-210573800	Weak transcription	Right Atrium	heart
18	chr1:210571200-210586200	Weak transcription	Colonic Mucosa	Colon
19	chr1:210571200-210592400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:210571400-210572600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:210571400-210573200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:210571400-210573600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:210571400-210573800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:210571400-210574200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:210571400-210591400	Weak transcription	Ovary	ovary
26	chr1:210571400-210641000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:210571800-210573400	Weak transcription	HSMM	muscle
28	chr1:210571800-210573800	Weak transcription	HSMMtube	muscle

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