Variant report

Variant	rs924592
Chromosome Location	chr5:75918738-75918739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2431347	1.00[CEU][hapmap];0.97[AMR][1000 genomes]
rs2431352	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2431358	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2431359	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2432181	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2432182	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2455226	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2516272	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2909892	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2910822	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs390086	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs402804	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs406217	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs421666	1.00[CEU][hapmap];0.97[AMR][1000 genomes]
rs463272	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs463815	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6453239	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6453240	1.00[CEU][hapmap];0.88[CHB][hapmap];0.98[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1031881	chr5:75917033-75946265	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs924592	TMPRSS3	trans	lymphoblastoid	seeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
2	chr5:75879200-75919000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:75880200-75933400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
5	chr5:75884400-75919200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr5:75884400-75919400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr5:75902600-75919200	Strong transcription	Primary T cells from cord blood	blood
8	chr5:75903800-75918800	Weak transcription	Fetal Kidney	kidney
9	chr5:75903800-75918800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:75903800-75936200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:75903800-75943600	Weak transcription	Spleen	Spleen
12	chr5:75905200-75919000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:75907600-75923000	Weak transcription	Placenta	Placenta
14	chr5:75907800-75934600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:75908000-75918800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:75908000-75919000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:75908000-75919000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:75908000-75928000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:75909000-75923200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr5:75909200-75923000	Weak transcription	Lung	lung
21	chr5:75910200-75919000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:75910200-75921200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:75911200-75923000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:75913400-75934600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:75914000-75919000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:75914000-75921800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:75914200-75919600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:75914200-75953800	Weak transcription	Colonic Mucosa	Colon
29	chr5:75914400-75919000	Weak transcription	Pancreas	Pancrea
30	chr5:75914400-75922600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:75914400-75922600	Weak transcription	Gastric	stomach
32	chr5:75914400-75922800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:75914400-75932800	Weak transcription	HepG2	liver
34	chr5:75914800-75919000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:75915000-75919400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:75915000-75923000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr5:75915000-75923200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:75915000-75923400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:75916200-75920400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr5:75916400-75921200	Weak transcription	Liver	Liver
41	chr5:75916400-75921600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr5:75916600-75918800	Weak transcription	K562	blood
43	chr5:75916800-75918800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:75916800-75919000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:75916800-75919200	Active TSS	NHLF	lung
46	chr5:75916800-75919600	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr5:75916800-75923200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr5:75917000-75920200	Strong transcription	Primary B cells from cord blood	blood
49	chr5:75917000-75921000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr5:75917200-75918800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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