Variant report

Variant	rs3776980
Chromosome Location	chr5:80527477-80527478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:80527262-80527586	Hela-S3	cervix:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACOT12-8	chr5:80521955-80529138	NONHSAT102436

Variant related genes	Relation type
CKMT2	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12657721	0.81[AMR][1000 genomes]
rs12658249	0.91[MEX][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes]
rs12659947	0.81[AMR][1000 genomes]
rs16878586	0.91[MEX][hapmap]
rs4704711	0.80[JPT][hapmap]
rs56270508	0.81[AMR][1000 genomes]
rs6898834	0.85[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80464200-80528400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:80465200-80528200	Weak transcription	Ovary	ovary
3	chr5:80491000-80528400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:80491200-80530000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:80491400-80528400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:80492000-80528600	Weak transcription	Left Ventricle	heart
7	chr5:80498000-80528800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:80498800-80530000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:80505400-80527800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:80506000-80530000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:80506400-80528000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:80507600-80528200	Weak transcription	HepG2	liver
13	chr5:80509000-80528400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:80509200-80528800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:80509400-80530000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:80510600-80528800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:80516400-80528600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:80520600-80530200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr5:80521000-80528600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr5:80522400-80530000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:80522600-80528800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr5:80522600-80530400	Weak transcription	Primary T cells from cord blood	blood
23	chr5:80522800-80528200	Weak transcription	Adipose Nuclei	Adipose
24	chr5:80523200-80528800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr5:80524200-80528200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:80524200-80528400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:80525800-80528200	Weak transcription	Brain Angular Gyrus	brain
28	chr5:80525800-80531000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:80526600-80531200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:80527000-80528600	Enhancers	Fetal Muscle Leg	muscle
31	chr5:80527000-80530000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:80527200-80528200	Enhancers	Fetal Heart	heart
34	chr5:80527200-80528200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr5:80527200-80528600	Enhancers	HSMMtube	muscle
36	chr5:80527400-80527800	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:80527400-80528000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr5:80527400-80528400	Enhancers	Fetal Muscle Trunk	muscle
39	chr5:80527400-80528600	Enhancers	Brain Substantia Nigra	brain

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