Variant report

Variant	rs2455226
Chromosome Location	chr5:75924974-75924975
allele	A/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];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2431352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431359	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs402804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs421666	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs463272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs463815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6453239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924592	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]

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
rs2455226	TMPRSS3	trans	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
2	chr5:75880200-75933400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
4	chr5:75903800-75936200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:75903800-75943600	Weak transcription	Spleen	Spleen
6	chr5:75907800-75934600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:75908000-75928000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:75913400-75934600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:75914200-75953800	Weak transcription	Colonic Mucosa	Colon
10	chr5:75914400-75932800	Weak transcription	HepG2	liver
11	chr5:75918000-75943400	Weak transcription	Fetal Intestine Small	intestine
12	chr5:75918200-75943600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:75918400-75927200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:75918400-75927800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:75919200-75926000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:75919200-75943600	Weak transcription	Fetal Intestine Large	intestine
17	chr5:75919200-75955400	Weak transcription	Fetal Kidney	kidney
18	chr5:75919400-75928200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:75919400-75938200	Weak transcription	Pancreas	Pancrea
20	chr5:75919400-75944200	Weak transcription	Fetal Lung	lung
21	chr5:75919600-75926000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:75921600-75926000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:75921600-75938000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:75921800-75926000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:75922000-75931000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:75922400-75928200	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr5:75922400-75929000	Strong transcription	Liver	Liver
28	chr5:75922600-75933400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr5:75922800-75938000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:75923000-75926200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:75923000-75933600	Weak transcription	GM12878-XiMat	blood
32	chr5:75923000-75938000	Weak transcription	Gastric	stomach
33	chr5:75923000-75938400	Weak transcription	Fetal Thymus	thymus
34	chr5:75923000-75944400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr5:75923200-75925200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:75923200-75926200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:75923200-75928600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:75923200-75933400	Strong transcription	Primary hematopoietic stem cells	blood
39	chr5:75923400-75928000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:75923400-75932400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:75923400-75934000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:75923400-75936200	Weak transcription	Fetal Stomach	stomach
43	chr5:75923600-75934400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:75923800-75933200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:75924000-75933400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr5:75924200-75927200	Weak transcription	Primary B cells from cord blood	blood
47	chr5:75924200-75929800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr5:75924200-75930000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:75924200-75943600	Weak transcription	Ovary	ovary
50	chr5:75924400-75926200	Weak transcription	Primary T cells from cord blood	blood

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