Variant report

Variant	rs7728222
Chromosome Location	chr5:49890507-49890508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10038842	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10039639	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10041633	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10043477	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10045122	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10052001	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070517	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10071272	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434558	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471888	1.00[ASN][1000 genomes]
rs10471893	1.00[ASN][1000 genomes]
rs10471940	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471956	1.00[ASN][1000 genomes]
rs10940423	0.94[EUR][1000 genomes]
rs10940424	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11738761	1.00[EUR][1000 genomes]
rs11741205	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745945	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12188654	0.82[EUR][1000 genomes]
rs12518710	1.00[ASN][1000 genomes]
rs12653803	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13159764	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13162921	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13164951	1.00[ASN][1000 genomes]
rs13355372	1.00[ASN][1000 genomes]
rs13355434	1.00[ASN][1000 genomes]
rs1375127	1.00[ASN][1000 genomes]
rs16884018	0.81[EUR][1000 genomes]
rs1839128	1.00[EUR][1000 genomes]
rs1900738	0.95[EUR][1000 genomes]
rs1972980	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1988613	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2034392	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034393	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2034394	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121979	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2166893	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2166894	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2354526	0.82[EUR][1000 genomes]
rs26066	1.00[ASN][1000 genomes]
rs26068	1.00[ASN][1000 genomes]
rs2697662	1.00[ASN][1000 genomes]
rs282549	1.00[ASN][1000 genomes]
rs282559	1.00[ASN][1000 genomes]
rs32377	1.00[ASN][1000 genomes]
rs32378	1.00[ASN][1000 genomes]
rs4029420	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4101529	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4282859	0.97[EUR][1000 genomes]
rs4415044	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4440312	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4865592	0.84[EUR][1000 genomes]
rs4865593	0.84[EUR][1000 genomes]
rs4865846	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865895	1.00[EUR][1000 genomes]
rs4865896	0.96[EUR][1000 genomes]
rs4866001	1.00[ASN][1000 genomes]
rs57079776	0.81[EUR][1000 genomes]
rs6450292	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6450301	0.82[EUR][1000 genomes]
rs6450359	1.00[ASN][1000 genomes]
rs6863575	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6867590	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6869356	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6872070	1.00[EUR][1000 genomes]
rs6879306	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886872	1.00[ASN][1000 genomes]
rs6888147	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093361	1.00[ASN][1000 genomes]
rs73112331	1.00[ASN][1000 genomes]
rs73112340	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7449019	1.00[ASN][1000 genomes]
rs7702541	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7709831	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710150	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711839	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7721050	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7730847	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734389	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736142	0.88[EUR][1000 genomes]
rs895801	1.00[ASN][1000 genomes]
rs921210	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv964850	chr5:49883635-49942856	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv14399	chr5:49885912-49934455	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7728222	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs7728222	PARP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49876800-49891400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:49885600-49890600	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr5:49885600-49890600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr5:49885600-49891400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:49885600-49891400	Enhancers	Dnd41	blood
6	chr5:49885600-49891800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:49885800-49891400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr5:49885800-49891800	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr5:49886200-49890600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr5:49886200-49891000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:49886200-49891400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr5:49886400-49890800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:49887200-49890800	Weak transcription	NHEK	skin
14	chr5:49888200-49890800	Enhancers	HMEC	breast
15	chr5:49888400-49892000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:49888600-49890800	Enhancers	NHDF-Ad	bronchial
17	chr5:49888600-49891000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:49888600-49891800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr5:49889200-49891000	Weak transcription	Osteobl	bone
20	chr5:49889400-49891600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr5:49889600-49891800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:49889800-49890800	Weak transcription	Hela-S3	cervix
23	chr5:49889800-49891400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:49890000-49890600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:49890200-49890600	Enhancers	Primary hematopoietic stem cells	blood
26	chr5:49890200-49891200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:49890400-49890600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:49890400-49890800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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