Variant report

Variant	rs6870725
Chromosome Location	chr5:80186922-80186923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10067194	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1017574	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs245338	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs245343	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs245345	0.87[CHB][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs245346	0.87[CHB][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs245351	0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs245362	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs245378	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs33002	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4704688	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs958575	0.84[AMR][1000 genomes];0.86[EUR][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	nsv882231	chr5:79984714-80187929	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv1799323	chr5:80179312-80219650	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6870725	DHFR	cis	Muscle Skeletal	GTEx
rs6870725	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80163200-80188400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:80167800-80187200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:80169600-80190600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:80171400-80196400	Weak transcription	Hela-S3	cervix
5	chr5:80173600-80208000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:80173800-80188600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr5:80174000-80187200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:80174000-80187200	Weak transcription	Right Ventricle	heart
9	chr5:80174000-80188200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:80174000-80188400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:80174000-80188400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:80174000-80188600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:80174000-80188600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:80174000-80190200	Weak transcription	Brain Anterior Caudate	brain
15	chr5:80174000-80190800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:80174000-80191200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr5:80174000-80191400	Weak transcription	Spleen	Spleen
18	chr5:80174000-80197000	Weak transcription	Left Ventricle	heart
19	chr5:80174200-80187200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr5:80174200-80187400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:80174200-80187800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:80174200-80188000	Weak transcription	Brain Angular Gyrus	brain
23	chr5:80174200-80192000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:80180400-80191200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:80180400-80215000	Weak transcription	Fetal Kidney	kidney
26	chr5:80180600-80187000	Weak transcription	Pancreas	Pancrea
27	chr5:80181600-80193200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:80181800-80188600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:80181800-80189400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:80181800-80189400	Weak transcription	A549	lung
31	chr5:80182000-80189400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr5:80182000-80191000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:80183600-80187200	Strong transcription	Fetal Stomach	stomach
34	chr5:80184200-80191800	Weak transcription	Gastric	stomach
35	chr5:80184600-80187200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr5:80185000-80187400	Strong transcription	Aorta	Aorta
37	chr5:80185000-80187400	Strong transcription	Thymus	Thymus
38	chr5:80185200-80187000	Strong transcription	Primary T cells from cord blood	blood
39	chr5:80185200-80187200	Strong transcription	Liver	Liver
40	chr5:80185800-80187200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:80185800-80187400	ZNF genes & repeats	Dnd41	blood
42	chr5:80185800-80187400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr5:80185800-80188000	Strong transcription	Primary B cells from cord blood	blood
44	chr5:80186200-80187200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:80186200-80187600	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr5:80186400-80187000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:80186400-80187200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:80186400-80187200	ZNF genes & repeats	Fetal Intestine Large	intestine
49	chr5:80186400-80187200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr5:80186400-80187400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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