Variant report

Variant	rs2564930
Chromosome Location	chr3:53017307-53017308
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	chr3:53010212..53012138-chr3:53016313..53018065,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2245424	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2257216	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2336670	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2336672	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2439434	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2465101	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2581803	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2581816	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581819	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581827	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2710313	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2710314	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2710326	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2710339	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2710346	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4515041	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6799185	0.80[EUR][1000 genomes]
rs6801235	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311485	0.80[ASN][1000 genomes]
rs9823697	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv3823	chr3:53003659-53051063	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2756989	chr3:53006055-53039455	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2759149	chr3:53006055-53039455	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv998445	chr3:53008146-53023199	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1001449	chr3:53009379-53039104	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv998180	chr3:53011207-53039267	Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1802390	chr3:53011741-53039205	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1008590	chr3:53011741-53039267	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1002814	chr3:53011741-53039665	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1011757	chr3:53012195-53039104	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2564930	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2564930	ITIH4-AS1	cis	Artery Tibial	GTEx
rs2564930	ITIH4-AS1	cis	Artery Aorta	GTEx
rs2564930	ITIH4-AS1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
2	chr3:52987200-53017400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:53002000-53017600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:53008400-53031000	Weak transcription	Hela-S3	cervix
5	chr3:53009800-53017600	Weak transcription	HepG2	liver
6	chr3:53012400-53017400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:53012600-53017600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:53012600-53019600	Weak transcription	Psoas Muscle	Psoas
9	chr3:53012600-53032600	Weak transcription	Pancreas	Pancrea
10	chr3:53014400-53017600	Weak transcription	Liver	Liver
11	chr3:53015600-53017600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:53015800-53017400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:53015800-53017800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:53015800-53018000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:53016000-53017800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr3:53016000-53017800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:53016000-53019000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr3:53016000-53019800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr3:53016200-53017800	Enhancers	Primary T cells from cord blood	blood
20	chr3:53016200-53019400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr3:53016200-53019800	Enhancers	Primary B cells from peripheral blood	blood
22	chr3:53016200-53029400	Weak transcription	Fetal Intestine Small	intestine
23	chr3:53016800-53017600	Enhancers	Primary B cells from cord blood	blood
24	chr3:53016800-53017600	Enhancers	Thymus	Thymus
25	chr3:53017000-53017400	Weak transcription	Brain Substantia Nigra	brain
26	chr3:53017000-53017600	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr3:53017000-53018000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:53017000-53018200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:53017000-53018200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr3:53017000-53018400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr3:53017000-53018400	Enhancers	Duodenum Mucosa	Duodenum
32	chr3:53017000-53018400	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr3:53017000-53018600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:53017000-53019000	Enhancers	Fetal Thymus	thymus
35	chr3:53017000-53019200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:53017000-53019200	Enhancers	Adipose Nuclei	Adipose
37	chr3:53017000-53020600	Enhancers	Dnd41	blood
38	chr3:53017200-53017400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr3:53017200-53017400	Active TSS	GM12878-XiMat	blood
40	chr3:53017200-53017800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:53017200-53019000	Enhancers	Primary hematopoietic stem cells	blood

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