Variant report

Variant	rs6887400
Chromosome Location	chr5:79958700-79958701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79950067..79952417-chr5:79958282..79961440,3	K562	blood:
2	chr5:79958590..79961048-chr5:80005503..80007376,2	K562	blood:
3	chr5:79955227..79957557-chr5:79958269..79961071,2	K562	blood:
4	chr5:79956607..79959193-chr5:79962502..79964568,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228716	Chromatin interaction
ENSG00000113318	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2081853	0.82[EUR][1000 genomes]
rs6151603	0.81[EUR][1000 genomes]
rs6151604	0.89[ASN][1000 genomes]
rs6151617	0.82[EUR][1000 genomes]
rs6151627	0.86[ASN][1000 genomes]
rs6151629	0.86[ASN][1000 genomes]
rs6151651	0.86[ASN][1000 genomes]
rs6151653	0.85[ASN][1000 genomes]
rs6151661	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6151670	0.84[ASN][1000 genomes]
rs6861850	0.83[ASN][1000 genomes]
rs6864493	0.85[ASN][1000 genomes]
rs73132417	0.89[ASN][1000 genomes]
rs7712332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv1792078	chr5:79953567-79962367	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv1831340	chr5:79953567-79962367	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv1851181	chr5:79953567-79962367	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	esv1826846	chr5:79956218-79961861	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1818797	chr5:79956218-79962367	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv10710	chr5:79956446-79964949	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6887400	DHFR	cis	Muscle Skeletal	GTEx
rs6887400	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79951200-79963200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:79951400-79963200	Weak transcription	Right Ventricle	heart
3	chr5:79951600-79959000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:79951600-79962600	Weak transcription	Esophagus	oesophagus
5	chr5:79951600-79963200	Weak transcription	Pancreas	Pancrea
6	chr5:79951600-79963400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:79951600-79963400	Weak transcription	Brain Germinal Matrix	brain
8	chr5:79951600-79963600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:79951600-79969200	Weak transcription	Stomach Mucosa	stomach
10	chr5:79951600-79972200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr5:79951600-80015600	Weak transcription	Small Intestine	intestine
12	chr5:79951800-79960200	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:79951800-79964000	Weak transcription	Brain Substantia Nigra	brain
14	chr5:79951800-79982800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:79952000-79959800	Weak transcription	HMEC	breast
16	chr5:79952000-79963800	Weak transcription	Fetal Heart	heart
17	chr5:79952200-79964200	Weak transcription	Brain Angular Gyrus	brain
18	chr5:79952200-79964200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr5:79952200-79964200	Weak transcription	NHLF	lung
20	chr5:79952200-79975400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:79952400-79959800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:79952400-79963200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:79952400-79963400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:79952400-79965000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:79952400-79967400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:79952400-79975400	Weak transcription	HSMMtube	muscle
27	chr5:79952400-79976600	Strong transcription	Fetal Thymus	thymus
28	chr5:79952400-79976800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr5:79952400-79983000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr5:79952600-79959000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr5:79952600-79959400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:79952600-79960600	Weak transcription	Hela-S3	cervix
33	chr5:79952600-79962200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr5:79952600-79963000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:79952600-79963200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:79952600-79963800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:79952600-79965000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:79952600-79985200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr5:79952600-79991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:79952800-79958800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:79952800-79959800	Weak transcription	HepG2	liver
42	chr5:79952800-79972200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:79953000-79958800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:79953000-79959200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:79953000-79966400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr5:79953200-79959200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:79953200-79963400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr5:79953200-79963800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr5:79953200-79964200	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr5:79953200-79964200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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