Variant report

Variant	rs27365
Chromosome Location	chr5:80034940-80034941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1650690	0.85[CEU][hapmap]
rs1650723	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1650734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1650735	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1650736	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs245397	0.80[AMR][1000 genomes]
rs245399	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245403	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs245408	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs26266	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs26268	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs26283	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32958	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs32994	0.81[EUR][1000 genomes]
rs33009	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs33010	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs33012	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs39628	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs42290	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6151616	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs836790	1.00[CEU][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs27365	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs27365	MSH3	cis	Whole Blood	GTEx
rs27365	MSH3	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79963600-80038600	Weak transcription	Right Ventricle	heart
2	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:79972400-80037000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
6	chr5:79998600-80051000	Weak transcription	Fetal Brain Male	brain
7	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:80000200-80038600	Weak transcription	Esophagus	oesophagus
9	chr5:80000400-80036800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:80000400-80036800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:80004000-80050400	Weak transcription	NHDF-Ad	bronchial
12	chr5:80009800-80039000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:80010600-80036800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:80016000-80038400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:80016000-80040600	Weak transcription	Small Intestine	intestine
16	chr5:80016200-80040600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:80016200-80040600	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:80016200-80043600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:80016400-80038200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:80016400-80050800	Weak transcription	Psoas Muscle	Psoas
21	chr5:80020200-80043600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:80022200-80040000	Weak transcription	K562	blood
23	chr5:80022800-80038000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:80022800-80038600	Weak transcription	Colonic Mucosa	Colon
25	chr5:80022800-80040600	Weak transcription	Spleen	Spleen
26	chr5:80022800-80041400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:80022800-80051200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:80023000-80036800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:80023000-80038000	Weak transcription	Left Ventricle	heart
30	chr5:80023000-80038400	Weak transcription	Fetal Muscle Leg	muscle
31	chr5:80023000-80038600	Weak transcription	Ovary	ovary
32	chr5:80023000-80038800	Weak transcription	Lung	lung
33	chr5:80023000-80040600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:80023000-80040600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr5:80023000-80040600	Weak transcription	Brain Hippocampus Middle	brain
36	chr5:80023000-80040600	Weak transcription	HUVEC	blood vessel
37	chr5:80023000-80041400	Weak transcription	Fetal Brain Female	brain
38	chr5:80023000-80043000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:80023000-80043200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:80023400-80038600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr5:80023600-80038800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:80023800-80037000	Weak transcription	Fetal Thymus	thymus
43	chr5:80024000-80038600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:80024000-80041400	Weak transcription	NH-A	brain
45	chr5:80024200-80036600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr5:80024200-80036600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:80024200-80038400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr5:80024200-80038400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:80024200-80038600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:80024200-80038600	Weak transcription	Fetal Kidney	kidney

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