Variant report

Variant	rs1338289
Chromosome Location	chr1:210519658-210519659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210518674..210520729-chr1:210534485..210536224,2	MCF-7	breast:
2	chr1:210518580..210522911-chr1:210544090..210547825,5	MCF-7	breast:
3	chr1:210519420..210522572-chr1:210544529..210548976,6	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction
ENSG00000054392	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1005174	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10489383	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs10489385	1.00[ASW][hapmap];0.82[CHD][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs10489386	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10863819	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863822	0.87[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10863825	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs11119458	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11119459	0.83[EUR][1000 genomes]
rs11119460	0.82[EUR][1000 genomes]
rs11119462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119473	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11119475	1.00[ASW][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11119485	1.00[AFR][1000 genomes]
rs12024862	1.00[AFR][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[MKK][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12049137	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12062126	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12087955	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12120970	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12134251	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12138216	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs12141780	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12143463	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1338288	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17016002	0.87[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2143591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2294843	1.00[AFR][1000 genomes]
rs2294851	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs2357435	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3753230	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs3765865	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3765866	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3765877	1.00[ASW][hapmap];0.86[CHD][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3765878	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3765886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3819985	1.00[MKK][hapmap]
rs4844520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4844996	0.86[AFR][1000 genomes]
rs4844997	1.00[ASW][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58469250	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58960429	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60154123	0.86[AFR][1000 genomes]
rs628908	1.00[MKK][hapmap]
rs650728	1.00[MKK][hapmap]
rs657370	0.83[EUR][1000 genomes]
rs701943	1.00[MKK][hapmap]
rs701944	1.00[MKK][hapmap]
rs7525927	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[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	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1338289	ELK4	cis	cerebellum	SCAN
rs1338289	DYRK3	cis	parietal	SCAN
rs1338289	SYT14	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210503600-210546800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:210513000-210540400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:210516800-210534400	Weak transcription	Fetal Lung	lung
4	chr1:210517000-210520000	Weak transcription	HSMMtube	muscle
5	chr1:210517000-210520000	Weak transcription	NH-A	brain
6	chr1:210517000-210531400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:210517000-210534400	Weak transcription	HSMM	muscle
8	chr1:210517200-210520200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:210517200-210520600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:210517200-210524400	Weak transcription	Lung	lung
11	chr1:210517200-210524600	Weak transcription	Ovary	ovary
12	chr1:210517200-210525400	Weak transcription	Thymus	Thymus
13	chr1:210517200-210534400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:210517200-210534400	Weak transcription	Brain Anterior Caudate	brain
15	chr1:210517200-210534600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:210517200-210535800	Weak transcription	Right Ventricle	heart
17	chr1:210517200-210536000	Weak transcription	Fetal Stomach	stomach
18	chr1:210517200-210536000	Weak transcription	Left Ventricle	heart
19	chr1:210517400-210520000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:210517400-210520000	Weak transcription	Aorta	Aorta
21	chr1:210517400-210525400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:210517400-210533200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:210517400-210534400	Weak transcription	Adipose Nuclei	Adipose
24	chr1:210517600-210519800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:210517600-210522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:210517600-210536000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:210517800-210519800	Weak transcription	GM12878-XiMat	blood
28	chr1:210517800-210522200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:210518200-210520000	Weak transcription	Osteobl	bone
30	chr1:210518600-210519800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:210518600-210534400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:210519600-210520600	Enhancers	Fetal Heart	heart

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