Variant report

Variant	rs17271763
Chromosome Location	chr5:68491410-68491411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68487593..68492001-chr5:68493438..68496143,4	K562	blood:
2	chr5:68473756..68475838-chr5:68491178..68492966,2	K562	blood:
3	chr5:68484125..68487092-chr5:68490544..68492644,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153044	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10454825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10940208	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1128761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188874	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12189395	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16875380	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17331590	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2069432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28616082	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846484	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3966728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41392244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56072942	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56101109	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56667192	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57047253	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58176819	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58725071	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59497209	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61626775	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61699334	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61743885	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66525615	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66595384	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67275234	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67548500	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67693452	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67821207	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67980996	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867050	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6890817	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767813	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767816	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767820	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767822	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767833	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72767837	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767849	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767855	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767860	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767861	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767863	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767864	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767865	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7709090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714908	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734513	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7736312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3445512	chr5:68472245-68495835	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17271763	TNPO1	cis	parietal	SCAN
rs17271763	CCDC125	cis	lung	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68485800-68493800	Weak transcription	Lung	lung
2	chr5:68486000-68498200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:68486000-68498600	Weak transcription	Left Ventricle	heart
4	chr5:68486000-68505800	Weak transcription	Ovary	ovary
5	chr5:68486000-68513600	Weak transcription	Gastric	stomach
6	chr5:68486200-68492000	Weak transcription	Fetal Brain Female	brain
7	chr5:68486200-68492200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:68486200-68494200	Weak transcription	Fetal Lung	lung
9	chr5:68486200-68494400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:68486200-68494600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr5:68486200-68494800	Weak transcription	Brain Substantia Nigra	brain
12	chr5:68486200-68496200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr5:68486200-68496200	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:68486200-68497000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:68486200-68497600	Weak transcription	Fetal Heart	heart
16	chr5:68486200-68497600	Weak transcription	Pancreas	Pancrea
17	chr5:68486200-68498200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:68486200-68498400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:68486200-68499200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:68486200-68499400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr5:68486200-68500200	Weak transcription	Thymus	Thymus
22	chr5:68486200-68502000	Weak transcription	Placenta	Placenta
23	chr5:68486200-68502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:68486200-68502600	Weak transcription	Small Intestine	intestine
25	chr5:68486200-68505200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:68486200-68509400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:68486200-68509400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:68486200-68509400	Weak transcription	HSMM	muscle
29	chr5:68486200-68512800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr5:68486400-68491800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:68486400-68491800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:68486400-68494400	Weak transcription	HMEC	breast
33	chr5:68486400-68494400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr5:68486400-68494600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr5:68486400-68494800	Weak transcription	Adipose Nuclei	Adipose
36	chr5:68486400-68496400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:68486400-68496800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:68486400-68502400	Weak transcription	NH-A	brain
39	chr5:68486400-68502600	Weak transcription	Fetal Kidney	kidney
40	chr5:68486400-68502600	Weak transcription	HUVEC	blood vessel
41	chr5:68486400-68512400	Weak transcription	Primary B cells from cord blood	blood
42	chr5:68486400-68512600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr5:68486400-68513000	Weak transcription	Brain Germinal Matrix	brain
44	chr5:68486400-68513000	Weak transcription	Fetal Intestine Large	intestine
45	chr5:68486400-68513000	Weak transcription	Osteobl	bone
46	chr5:68486600-68491800	Weak transcription	HepG2	liver
47	chr5:68486600-68497200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:68486600-68502600	Weak transcription	NHLF	lung
49	chr5:68486600-68509200	Weak transcription	NHDF-Ad	bronchial
50	chr5:68487400-68508200	Strong transcription	HUES48 Cell Line	embryonic stem cell

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