Variant report

Variant	rs1650735
Chromosome Location	chr5:80002739-80002740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
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	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650736	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245394	0.80[AMR][1000 genomes]
rs245397	0.82[AMR][1000 genomes]
rs245399	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs245400	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs245403	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs245408	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs26266	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs26268	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs26283	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs27365	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28026	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs32958	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33009	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs33010	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs33012	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs39628	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs42290	0.94[AMR][1000 genomes];0.86[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:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1650735	MSH3	cis	Whole Blood	GTEx
rs1650735	MSH3	cis	Thyroid	GTEx
rs1650735	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79951600-80015600	Weak transcription	Small Intestine	intestine
2	chr5:79956400-80015600	Weak transcription	Psoas Muscle	Psoas
3	chr5:79962800-80015600	Weak transcription	A549	lung
4	chr5:79963600-80038600	Weak transcription	Right Ventricle	heart
5	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:79965000-80021400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:79969600-80010600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:79971600-80022200	Weak transcription	HMEC	breast
9	chr5:79971800-80003400	Weak transcription	NHDF-Ad	bronchial
10	chr5:79971800-80015400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:79972400-80010400	Weak transcription	NHEK	skin
13	chr5:79972400-80037000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:79973200-80021600	Weak transcription	NH-A	brain
15	chr5:79973400-80008800	Weak transcription	Brain Anterior Caudate	brain
16	chr5:79974000-80003000	Weak transcription	Fetal Heart	heart
17	chr5:79974000-80021200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:79975200-80022800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:79975600-80015200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:79975600-80022000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:79975800-80002800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:79975800-80004400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:79975800-80007000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:79975800-80008800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:79975800-80009200	Weak transcription	Pancreas	Pancrea
26	chr5:79975800-80015600	Weak transcription	Brain Substantia Nigra	brain
27	chr5:79975800-80015800	Weak transcription	Fetal Brain Female	brain
28	chr5:79976000-80010400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:79976600-80003200	Weak transcription	Left Ventricle	heart
30	chr5:79979200-80013800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:79979800-80009000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr5:79979800-80015600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:79980000-80015800	Weak transcription	Fetal Kidney	kidney
34	chr5:79980200-80002800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr5:79980600-80003000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:79980600-80005800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:79981400-80003200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:79983400-80021600	Weak transcription	Brain Angular Gyrus	brain
39	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
40	chr5:79986200-80004400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:79986400-80002800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:79992400-80021000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:79994400-80016000	Weak transcription	Colon Smooth Muscle	Colon
44	chr5:79995800-80007800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr5:79997000-80009600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr5:79997400-80009200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr5:79998200-80003200	Weak transcription	Right Atrium	heart
48	chr5:79998400-80002800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr5:79998400-80002800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:79998400-80004200	Weak transcription	Fetal Muscle Trunk	muscle

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