Variant report

Variant	rs9925950
Chromosome Location	chr16:77234004-77234005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:77223287..77227235-chr16:77231893..77237199,5	MCF-7	breast:
2	chr16:77231454..77233524-chr16:77233775..77237585,4	MCF-7	breast:
3	chr16:77223627..77226316-chr16:77230976..77234622,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103111	Chromatin interaction
ENSG00000205078	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11865641	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12444706	0.83[ASN][1000 genomes]
rs12444881	0.86[ASN][1000 genomes]
rs12448895	0.82[ASN][1000 genomes]
rs12599030	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2161716	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2232493	0.85[ASN][1000 genomes]
rs2278046	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278047	0.85[ASN][1000 genomes]
rs2278048	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278049	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2343035	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2343036	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4887894	0.88[ASN][1000 genomes]
rs4887896	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4888606	0.88[ASN][1000 genomes]
rs4888608	0.86[ASN][1000 genomes]
rs56743953	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59418549	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61024035	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61032790	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61267588	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6564411	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7188097	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74027187	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74027188	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8055551	0.85[ASN][1000 genomes]
rs8061864	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8398	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9928151	0.92[ASN][1000 genomes]
rs9930815	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065343	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv542965	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1055234	chr16:77003426-77467286	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv1062349	chr16:77039764-77458731	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv542967	chr16:77039764-77458731	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv1066258	chr16:77229953-77521919	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv542968	chr16:77229953-77521919	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9925950	SYCE1L	cis	Muscle Skeletal	GTEx
rs9925950	RP11-538I12.2	cis	Esophagus Muscularis	GTEx
rs9925950	SYCE1L	cis	Nerve Tibial	GTEx
rs9925950	SYCE1L	cis	Thyroid	GTEx
rs9925950	SYCE1L	cis	Artery Aorta	GTEx
rs9925950	SYCE1L	cis	Esophagus Muscularis	GTEx
rs9925950	SYCE1L	cis	Stomach	GTEx
rs9925950	SYCE1L	cis	Adipose Subcutaneous	GTEx
rs9925950	SYCE1L	cis	Skin Sun Exposed Lower leg	GTEx
rs9925950	MON1B	Cis_1M	lymphoblastoid	RTeQTL
rs9925950	SYCE1L	cis	lung	GTEx
rs9925950	SYCE1L	cis	Whole Blood	GTEx
rs9925950	SYCE1L	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77226200-77240400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr16:77226400-77240200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr16:77226600-77234200	Strong transcription	Fetal Muscle Leg	muscle
4	chr16:77226600-77235000	Weak transcription	Psoas Muscle	Psoas
5	chr16:77226600-77235600	Strong transcription	Fetal Thymus	thymus
6	chr16:77226800-77234600	Strong transcription	Fetal Muscle Trunk	muscle
7	chr16:77226800-77235200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr16:77226800-77235600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:77226800-77235600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr16:77226800-77235600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr16:77227000-77235600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr16:77227000-77235600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr16:77227000-77235600	Strong transcription	Liver	Liver
14	chr16:77227000-77235800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr16:77227000-77236200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr16:77227000-77236600	Strong transcription	Primary T cells from cord blood	blood
17	chr16:77227000-77246000	Weak transcription	Fetal Heart	heart
18	chr16:77227200-77234200	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr16:77227200-77234600	Strong transcription	Fetal Stomach	stomach
20	chr16:77227200-77235600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr16:77227200-77235600	Strong transcription	Placenta	Placenta
22	chr16:77227200-77245800	Weak transcription	Fetal Kidney	kidney
23	chr16:77227200-77247200	Weak transcription	Hela-S3	cervix
24	chr16:77227400-77235600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr16:77227600-77235600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr16:77227800-77234200	Weak transcription	Fetal Brain Male	brain
27	chr16:77227800-77234400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr16:77227800-77235000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr16:77227800-77236600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr16:77228200-77235600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr16:77228600-77234200	Strong transcription	Lung	lung
32	chr16:77228600-77234200	Strong transcription	Dnd41	blood
33	chr16:77228600-77235200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr16:77228600-77235200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr16:77228800-77235600	Strong transcription	Fetal Intestine Large	intestine
36	chr16:77229000-77235600	Strong transcription	Primary B cells from cord blood	blood
37	chr16:77229200-77234200	Strong transcription	Spleen	Spleen
38	chr16:77229200-77235200	Strong transcription	GM12878-XiMat	blood
39	chr16:77230000-77235600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr16:77230200-77235600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:77230600-77235400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr16:77231000-77235600	Strong transcription	Brain Hippocampus Middle	brain
43	chr16:77231200-77235200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr16:77231400-77235600	Strong transcription	Primary hematopoietic stem cells	blood
45	chr16:77231400-77235600	Strong transcription	Brain Cingulate Gyrus	brain
46	chr16:77233000-77236400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr16:77233200-77235400	Weak transcription	Stomach Mucosa	stomach
48	chr16:77233200-77243400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr16:77233200-77245600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr16:77233200-77245600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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