Variant report

Variant	rs1129680
Chromosome Location	chr16:77236264-77236265
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:77235549..77237058-chr16:77254085..77256585,2	K562	blood:
2	chr16:77223287..77227235-chr16:77231893..77237199,5	MCF-7	breast:
3	chr16:77231454..77233524-chr16:77233775..77237585,4	MCF-7	breast:
4	chr16:77223922..77226373-chr16:77234671..77237150,2	MCF-7	breast:
5	chr16:77228552..77231268-chr16:77235268..77236824,2	MCF-7	breast:
6	chr16:77234733..77236647-chr16:77240171..77241998,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205078	Chromatin interaction
ENSG00000103111	Chromatin interaction
ENSG00000226348	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7204495	0.81[CHD][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1129680	KCNK5	trans	cerebellum	SCAN
rs1129680	TXNL4B	cis	parietal	SCAN
rs1129680	MON1B	cis	parietal	SCAN
rs1129680	RP11-538I12.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:115 , 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	chr16:77227000-77236600	Strong transcription	Primary T cells from cord blood	blood
4	chr16:77227000-77246000	Weak transcription	Fetal Heart	heart
5	chr16:77227200-77245800	Weak transcription	Fetal Kidney	kidney
6	chr16:77227200-77247200	Weak transcription	Hela-S3	cervix
7	chr16:77227800-77236600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr16:77233000-77236400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr16:77233200-77243400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr16:77233200-77245600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr16:77233200-77245600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr16:77233200-77245800	Weak transcription	NHEK	skin
13	chr16:77233400-77236600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr16:77233400-77236600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr16:77233400-77237600	Weak transcription	NHDF-Ad	bronchial
16	chr16:77233400-77238000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr16:77233400-77238400	Weak transcription	NHLF	lung
18	chr16:77233400-77239600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr16:77233400-77240000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr16:77233400-77245000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr16:77233400-77245400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr16:77233400-77245600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr16:77233400-77245600	Weak transcription	HMEC	breast
24	chr16:77233400-77245600	Weak transcription	NH-A	brain
25	chr16:77233400-77246000	Weak transcription	Aorta	Aorta
26	chr16:77233400-77246000	Weak transcription	Brain Angular Gyrus	brain
27	chr16:77233400-77246000	Weak transcription	Brain Substantia Nigra	brain
28	chr16:77233600-77240200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr16:77233800-77236400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr16:77233800-77237400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr16:77233800-77237400	Weak transcription	Colonic Mucosa	Colon
32	chr16:77233800-77237600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr16:77233800-77238600	Weak transcription	Gastric	stomach
34	chr16:77233800-77239400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr16:77233800-77239600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr16:77233800-77240000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr16:77233800-77240000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr16:77233800-77245400	Weak transcription	A549	lung
39	chr16:77233800-77245600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr16:77233800-77245600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr16:77233800-77245600	Weak transcription	Brain Germinal Matrix	brain
42	chr16:77233800-77245600	Weak transcription	Fetal Lung	lung
43	chr16:77233800-77245600	Weak transcription	HUVEC	blood vessel
44	chr16:77233800-77245800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr16:77233800-77245800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr16:77233800-77245800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr16:77233800-77245800	Weak transcription	Fetal Brain Female	brain
48	chr16:77233800-77245800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr16:77233800-77246000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr16:77233800-77246000	Weak transcription	HSMMtube	muscle

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