Variant report

Variant	rs16940987
Chromosome Location	chr15:59353863-59353864
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59352012..59354912-chr15:59357876..59359782,2	K562	blood:
2	chr15:59224343..59226542-chr15:59353836..59355636,2	K562	blood:
3	chr15:59352406..59354912-chr15:59358282..59360921,2	K562	blood:

Variant related genes	Relation type
ENSG00000137776	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10431762	0.88[AFR][1000 genomes]
rs10851642	0.80[AFR][1000 genomes]
rs11855536	0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs12050865	0.85[AFR][1000 genomes]
rs12438128	0.85[AFR][1000 genomes]
rs12438962	0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs12906212	0.84[YRI][hapmap];0.88[AFR][1000 genomes]
rs12907548	0.86[LWK][hapmap];0.82[YRI][hapmap]
rs12915899	0.85[LWK][hapmap]
rs1374155	0.82[LWK][hapmap];0.84[YRI][hapmap]
rs1446237	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs1446238	0.82[YRI][hapmap];0.87[AFR][1000 genomes]
rs16940998	0.81[LWK][hapmap]
rs17236383	0.85[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs17302142	0.85[AFR][1000 genomes]
rs17302191	0.80[YRI][hapmap]
rs1971181	0.88[AFR][1000 genomes]
rs1975534	0.85[AFR][1000 genomes]
rs2414618	0.84[AFR][1000 genomes]
rs34859729	0.80[AFR][1000 genomes]
rs35210199	0.84[AFR][1000 genomes]
rs35658945	0.84[AFR][1000 genomes]
rs35769647	0.95[AFR][1000 genomes]
rs57557135	0.92[AFR][1000 genomes]
rs59282449	0.84[AFR][1000 genomes]
rs59514650	0.89[AFR][1000 genomes]
rs60262196	0.87[AFR][1000 genomes]
rs60741546	0.89[AFR][1000 genomes]
rs61022867	0.81[AFR][1000 genomes]
rs62002543	0.93[AFR][1000 genomes]
rs62002544	0.87[AFR][1000 genomes]
rs71480503	0.93[AFR][1000 genomes]
rs8028752	0.92[ASW][hapmap];0.81[LWK][hapmap];0.94[YRI][hapmap]
rs8030246	0.83[YRI][hapmap]
rs8030323	0.83[AFR][1000 genomes]
rs8031390	0.80[AFR][1000 genomes]
rs877269	0.84[YRI][hapmap];0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv510663	chr15:59310676-59370041	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
8	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16940987	CCNB2	cis	cerebellum	SCAN
rs16940987	GCNT3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59283800-59359000	Weak transcription	Fetal Brain Male	brain
2	chr15:59305400-59354400	Weak transcription	Gastric	stomach
3	chr15:59308400-59358000	Weak transcription	Spleen	Spleen
4	chr15:59309200-59359000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:59323600-59359000	Weak transcription	Esophagus	oesophagus
6	chr15:59325000-59354800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:59326400-59365200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:59332400-59358200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:59335800-59354400	Weak transcription	Psoas Muscle	Psoas
10	chr15:59342400-59364400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:59342400-59365400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:59344200-59356200	Strong transcription	K562	blood
13	chr15:59344200-59364400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:59344200-59364400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr15:59344400-59354600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr15:59344400-59356200	Strong transcription	A549	lung
17	chr15:59344400-59358000	Weak transcription	Right Ventricle	heart
18	chr15:59344400-59363200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr15:59344400-59364200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:59344400-59392800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr15:59344600-59363200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr15:59344600-59363800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:59344600-59363800	Strong transcription	Fetal Thymus	thymus
24	chr15:59344800-59354600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr15:59344800-59354800	Strong transcription	Osteobl	bone
26	chr15:59344800-59355000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:59344800-59355000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:59344800-59363000	Strong transcription	Hela-S3	cervix
29	chr15:59344800-59363200	Strong transcription	Primary B cells from cord blood	blood
30	chr15:59344800-59363800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr15:59344800-59363800	Strong transcription	Dnd41	blood
32	chr15:59344800-59364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:59344800-59364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:59344800-59366400	Strong transcription	Placenta	Placenta
35	chr15:59344800-59370400	Strong transcription	Primary T cells from cord blood	blood
36	chr15:59345000-59355000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr15:59345000-59356000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr15:59345000-59363000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:59345200-59354800	Strong transcription	Liver	Liver
40	chr15:59345200-59355600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:59345200-59355800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:59345200-59356600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr15:59345200-59363000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr15:59345200-59363800	Strong transcription	HSMM	muscle
45	chr15:59345400-59354200	Strong transcription	Adipose Nuclei	Adipose
46	chr15:59345400-59363000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:59345400-59363800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr15:59345400-59365200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:59345800-59365200	Strong transcription	Fetal Intestine Large	intestine
50	chr15:59346000-59354600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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