Variant report

Variant	rs2516272
Chromosome Location	chr5:75933581-75933582
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75903037..75905690-chr5:75932365..75935110,2	K562	blood:
2	chr5:75926553..75929296-chr5:75932910..75934652,2	K562	blood:

Variant related genes	Relation type
ENSG00000249713	Chromatin interaction
ENSG00000145703	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2069686	1.00[YRI][hapmap]
rs2431347	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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]
rs2432181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455226	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	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs402804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[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];1.00[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	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs463815	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6453239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924592	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]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv1017025	chr5:75926278-75946265	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1035135	chr5:75927027-76092058	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2516272	TMPRSS3	trans	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
2	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
3	chr5:75903800-75936200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:75903800-75943600	Weak transcription	Spleen	Spleen
5	chr5:75907800-75934600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:75913400-75934600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:75914200-75953800	Weak transcription	Colonic Mucosa	Colon
8	chr5:75918000-75943400	Weak transcription	Fetal Intestine Small	intestine
9	chr5:75918200-75943600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:75919200-75943600	Weak transcription	Fetal Intestine Large	intestine
11	chr5:75919200-75955400	Weak transcription	Fetal Kidney	kidney
12	chr5:75919400-75938200	Weak transcription	Pancreas	Pancrea
13	chr5:75919400-75944200	Weak transcription	Fetal Lung	lung
14	chr5:75921600-75938000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:75922800-75938000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:75923000-75933600	Weak transcription	GM12878-XiMat	blood
17	chr5:75923000-75938000	Weak transcription	Gastric	stomach
18	chr5:75923000-75938400	Weak transcription	Fetal Thymus	thymus
19	chr5:75923000-75944400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr5:75923400-75934000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:75923400-75936200	Weak transcription	Fetal Stomach	stomach
22	chr5:75923600-75934400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:75924200-75943600	Weak transcription	Ovary	ovary
24	chr5:75924800-75936200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:75926200-75938000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr5:75926200-75943800	Strong transcription	Primary T cells from cord blood	blood
27	chr5:75926600-75934200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr5:75928400-75937000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:75929400-75943800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr5:75929800-75934000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr5:75929800-75934400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr5:75929800-75938000	Weak transcription	NH-A	brain
33	chr5:75929800-75943800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:75929800-75945400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr5:75930400-75944400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:75931400-75933600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr5:75931400-75935000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:75931400-75943800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:75931600-75943600	Weak transcription	Lung	lung
40	chr5:75932200-75936200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:75932200-75945400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:75932400-75933600	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:75932400-75933600	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr5:75932600-75938000	Weak transcription	NHLF	lung
45	chr5:75932800-75933800	Enhancers	HepG2	liver
46	chr5:75932800-75935200	Strong transcription	Placenta	Placenta
47	chr5:75932800-75937600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr5:75932800-75938000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr5:75933200-75934200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:75933200-75934200	Enhancers	Liver	Liver

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