Variant report

Variant	rs2899637
Chromosome Location	chr15:59268410-59268411
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	chr15:59225292..59227071-chr15:59266536..59268514,2	K562	blood:
2	chr15:59266779..59268422-chr15:59365883..59367476,2	K562	blood:

Variant related genes	Relation type
ENSG00000137776	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12905422	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs1693534	0.83[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs17236341	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2414615	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2414617	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35473102	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4774316	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775108	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4775109	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61668497	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62002471	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7169181	0.82[JPT][hapmap]
rs7171316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8024549	0.81[JPT][hapmap]
rs8031016	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
3	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv904271	chr15:59249584-59393011	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv520679	chr15:59268410-59376531	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv520872	chr15:59268410-59395184	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2899637	NEDD4	cis	cerebellum	SCAN
rs2899637	FAM63B	cis	parietal	SCAN
rs2899637	GCNT3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59265600-59279200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr15:59266000-59274400	Enhancers	Primary B cells from peripheral blood	blood
3	chr15:59267000-59268800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr15:59267000-59268800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:59267000-59269000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr15:59267200-59268600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr15:59267200-59268800	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr15:59267200-59268800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:59267200-59269000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:59267400-59268600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr15:59267400-59268800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:59267400-59268800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr15:59267400-59268800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr15:59267400-59268800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr15:59267400-59268800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr15:59267400-59269000	Enhancers	Primary hematopoietic stem cells	blood
17	chr15:59267400-59269000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:59267400-59269000	Enhancers	HUVEC	blood vessel
19	chr15:59267400-59269200	Enhancers	Primary B cells from cord blood	blood
20	chr15:59267800-59268600	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr15:59267800-59268600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:59267800-59268800	Enhancers	Primary T cells from cord blood	blood
23	chr15:59268000-59271400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:59268000-59271600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr15:59268000-59273800	Weak transcription	Adipose Nuclei	Adipose
26	chr15:59268400-59268800	Enhancers	GM12878-XiMat	blood
27	chr15:59268400-59272400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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