Variant report

Variant	rs249208
Chromosome Location	chr5:79865080-79865081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79858408..79862630-chr5:79863192..79865325,4	MCF-7	breast:
2	chr5:79859883..79861719-chr5:79862893..79865594,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs118526	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs249204	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249209	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249218	0.81[EUR][1000 genomes]
rs249219	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027183	chr5:79837249-79876229	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1021286	chr5:79844255-79876229	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1025796	chr5:79844255-79880441	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1034832	chr5:79844255-79892075	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1034384	chr5:79846926-79876229	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1021853	chr5:79847376-79876229	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1027663	chr5:79855710-79876229	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1020051	chr5:79855710-79879770	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1029820	chr5:79855710-79880441	Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1035021	chr5:79855710-79892075	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1022154	chr5:79855710-79897516	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs249208	DHFR	cis	Muscle Skeletal	GTEx
rs249208	DHFR	cis	Whole Blood	GTEx
rs249208	ANKRD34B	cis	Whole Blood	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79863800-79866400	Active TSS	Brain Anterior Caudate	brain
2	chr5:79864400-79866600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr5:79864600-79865200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr5:79864600-79865800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
5	chr5:79864600-79866600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr5:79864600-79866600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr5:79864600-79866600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:79864600-79866600	Bivalent Enhancer	Fetal Brain Male	brain
9	chr5:79864600-79866800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:79864800-79865200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:79864800-79865200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr5:79864800-79865200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
13	chr5:79864800-79865200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr5:79864800-79865200	Bivalent Enhancer	Fetal Stomach	stomach
15	chr5:79864800-79865200	Bivalent Enhancer	HMEC	breast
16	chr5:79864800-79865400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
17	chr5:79864800-79865400	Bivalent Enhancer	Adipose Nuclei	Adipose
18	chr5:79864800-79865400	Enhancers	Liver	Liver
19	chr5:79864800-79865400	Bivalent Enhancer	Esophagus	oesophagus
20	chr5:79864800-79865400	Bivalent Enhancer	Stomach Mucosa	stomach
21	chr5:79864800-79865600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr5:79864800-79865600	Bivalent Enhancer	Lung	lung
23	chr5:79864800-79865600	Enhancers	Pancreas	Pancrea
24	chr5:79864800-79865800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:79864800-79865800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
26	chr5:79864800-79865800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr5:79864800-79865800	Bivalent Enhancer	Placenta	Placenta
28	chr5:79864800-79865800	Bivalent Enhancer	Fetal Thymus	thymus
29	chr5:79864800-79865800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
30	chr5:79864800-79866000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
31	chr5:79864800-79866200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr5:79864800-79866400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:79864800-79866400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:79864800-79866400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
35	chr5:79864800-79866600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr5:79864800-79866600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:79864800-79866600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr5:79864800-79866600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
39	chr5:79864800-79866600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr5:79864800-79866600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:79864800-79866600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
42	chr5:79864800-79866600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:79864800-79866600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:79864800-79866600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:79864800-79866600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
46	chr5:79865000-79865200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr5:79865000-79865200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
48	chr5:79865000-79865200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
49	chr5:79865000-79865200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
50	chr5:79865000-79865200	Flanking Active TSS	Fetal Heart	heart

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