Variant report

Variant	rs10513219
Chromosome Location	chr3:143534874-143534875
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	chr3:143534241..143536547-chr3:143539436..143542162,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11710427	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11917152	0.82[CEU][hapmap];0.85[CHB][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11918501	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11919227	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1823221	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2011026	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2361200	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55654258	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62268880	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62268900	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66585826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6773298	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6794755	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6798159	1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67981921	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6806661	0.87[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs72995501	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73158100	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7641634	0.87[CEU][hapmap];0.85[CHB][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs7641674	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv3418674	chr3:143457005-143558357	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1001076	chr3:143513526-143547076	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv536747	chr3:143513526-143547076	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10513219	TFDP2	cis	parietal	SCAN
rs10513219	GMPR	trans	lymphoblastoid	seeQTL
rs10513219	ENG	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143514200-143544200	Weak transcription	Primary T cells from cord blood	blood
2	chr3:143529600-143540600	Weak transcription	Brain Angular Gyrus	brain
3	chr3:143529600-143543800	Weak transcription	Stomach Mucosa	stomach
4	chr3:143530000-143538800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:143530600-143539800	Weak transcription	Ovary	ovary
6	chr3:143530600-143540600	Weak transcription	Placenta	Placenta
7	chr3:143530800-143540800	Weak transcription	Fetal Stomach	stomach
8	chr3:143531000-143539800	Weak transcription	Adipose Nuclei	Adipose
9	chr3:143531000-143543200	Weak transcription	NHDF-Ad	bronchial
10	chr3:143531400-143539000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:143531800-143539400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:143531800-143543200	Weak transcription	Aorta	Aorta
13	chr3:143533600-143535200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr3:143533600-143543200	Weak transcription	Fetal Lung	lung
15	chr3:143533800-143539400	Weak transcription	Spleen	Spleen
16	chr3:143533800-143540600	Weak transcription	Primary B cells from cord blood	blood
17	chr3:143533800-143543200	Weak transcription	Right Atrium	heart
18	chr3:143534000-143539800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:143534000-143540600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:143534200-143539600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:143534200-143539800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:143534200-143540000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:143534400-143535400	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr3:143534400-143539400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:143534400-143539400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:143534400-143539800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:143534400-143540600	Weak transcription	Fetal Thymus	thymus

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