Variant report

Variant	rs1144480
Chromosome Location	chr10:44848921-44848922
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:44847947..44849950-chr10:44851520..44853387,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1107008	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1144472	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1144474	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1144475	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1144476	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1144477	0.91[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1144478	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1144479	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144482	0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1144485	0.80[AMR][1000 genomes]
rs1147877	0.81[CEU][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1147878	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1147879	0.91[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1147880	0.91[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1147881	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1147882	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1147887	0.92[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs2505741	0.83[CHD][hapmap];0.86[MKK][hapmap];0.80[AMR][1000 genomes]
rs2505742	0.80[AMR][1000 genomes]
rs874304	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs920173	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs920174	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs928565	0.81[CHD][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs982098	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038511	chr10:44596885-44870030	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1052337	chr10:44821390-44865015	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
3	nsv1054649	chr10:44848921-44889713	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1144480	RET	cis	cerebellum	SCAN
rs1144480	ANTXRL	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44838600-44867400	Weak transcription	Spleen	Spleen
2	chr10:44846600-44850800	Enhancers	Fetal Lung	lung
3	chr10:44847000-44852000	Enhancers	Pancreas	Pancrea
4	chr10:44847200-44849000	Enhancers	Fetal Stomach	stomach
5	chr10:44847200-44849400	Enhancers	Right Ventricle	heart
6	chr10:44847800-44849200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:44848000-44851800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr10:44848000-44851800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr10:44848200-44851400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr10:44848200-44852200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr10:44848200-44853600	Weak transcription	Brain Substantia Nigra	brain
12	chr10:44848200-44858600	Weak transcription	Psoas Muscle	Psoas
13	chr10:44848200-44864600	Weak transcription	Fetal Kidney	kidney
14	chr10:44848200-44865000	Weak transcription	Osteobl	bone
15	chr10:44848400-44851800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:44848400-44851800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr10:44848400-44865000	Weak transcription	Right Atrium	heart
18	chr10:44848400-44867400	Weak transcription	Adipose Nuclei	Adipose
19	chr10:44848400-44867600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr10:44848600-44849000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr10:44848600-44849200	Weak transcription	Left Ventricle	heart
22	chr10:44848600-44853800	Weak transcription	Ovary	ovary
23	chr10:44848800-44851600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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