Variant report

Variant	rs7726225
Chromosome Location	chr5:49989733-49989734
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	chr5:49989186..49991048-chr5:49992537..49995314,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10052372	0.86[EUR][1000 genomes]
rs11950506	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11952107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11954064	0.94[AMR][1000 genomes]
rs11955651	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11955934	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11959326	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13153852	0.89[AMR][1000 genomes]
rs13155662	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13156735	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13157079	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13159045	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13159239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13161225	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13162738	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13163470	0.87[EUR][1000 genomes]
rs13163802	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13166819	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13169153	0.87[EUR][1000 genomes]
rs13169200	1.00[AMR][1000 genomes]
rs13171248	0.81[AMR][1000 genomes]
rs13174498	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13176737	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13180485	0.89[AMR][1000 genomes]
rs13181031	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13181117	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13183910	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13186653	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13189183	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13190144	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16886309	0.87[EUR][1000 genomes]
rs1968637	0.81[AMR][1000 genomes]
rs2354531	0.81[AMR][1000 genomes]
rs34183555	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34264957	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34414061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34443769	1.00[AMR][1000 genomes]
rs34677483	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34758774	0.96[EUR][1000 genomes]
rs34827507	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34855203	1.00[EUR][1000 genomes]
rs35128589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35210389	1.00[AMR][1000 genomes]
rs35292338	1.00[AMR][1000 genomes]
rs35347195	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35473824	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35596019	1.00[AMR][1000 genomes]
rs41270305	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6859621	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6880398	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6883701	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6888271	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6888315	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6892149	0.89[AMR][1000 genomes]
rs71615975	0.83[AMR][1000 genomes]
rs71615978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71615981	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71615983	0.87[EUR][1000 genomes]
rs71615984	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71615986	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71615988	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71615990	0.83[EUR][1000 genomes]
rs71615991	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71631479	1.00[AMR][1000 genomes]
rs7717073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7723395	0.81[AMR][1000 genomes]
rs7730188	1.00[AMR][1000 genomes]
rs7733931	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	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
4	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
5	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
6	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
7	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
8	nsv818352	chr5:49958221-50017724	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv537759	chr5:49986171-50033616	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv1030068	chr5:49986171-50047352	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv537760	chr5:49986171-50047352	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	nsv521214	chr5:49988020-50037381	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv462160	chr5:49988020-50058043	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv598109	chr5:49988020-50058043	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	nsv598110	chr5:49988020-50089919	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv819124	chr5:49989212-49993721	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv462162	chr5:49989701-50040778	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv598111	chr5:49989701-50040778	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv598112	chr5:49989701-50062611	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	nsv462163	chr5:49989701-50088317	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
26	nsv598113	chr5:49989701-50088317	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7726225	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49968800-49990400	Weak transcription	Small Intestine	intestine
2	chr5:49976800-50000000	Weak transcription	Fetal Stomach	stomach
3	chr5:49977800-49990600	Weak transcription	Pancreas	Pancrea
4	chr5:49978200-49995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:49979000-49995200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:49979400-50006600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:49980800-49995000	Weak transcription	Thymus	Thymus
8	chr5:49981400-49992600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr5:49982600-49992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:49982800-49997000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:49983000-49998800	Weak transcription	Lung	lung
12	chr5:49983200-49994200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr5:49983400-50006800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:49986000-50006600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:49986800-49989800	Weak transcription	Fetal Intestine Large	intestine
16	chr5:49987200-49989800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:49987200-49993200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr5:49987200-49994800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:49987400-49994800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr5:49987400-49995200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:49987600-49990600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr5:49987600-49991000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:49987600-49991800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:49987600-49995000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:49987600-50001600	Weak transcription	Dnd41	blood
26	chr5:49987800-49990000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:49987800-49990200	Enhancers	GM12878-XiMat	blood
28	chr5:49987800-49990600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr5:49987800-49995000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr5:49987800-49998200	Weak transcription	Primary B cells from cord blood	blood
31	chr5:49987800-49998800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:49988000-49995400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:49988200-49992400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr5:49988400-49991200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:49988600-49991400	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr5:49989000-49991000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:49989000-49997600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr5:49989200-49990000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr5:49989200-49990200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:49989200-49990400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:49989200-49998000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:49989400-49990400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr5:49989400-49990600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:49989400-49992200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr5:49989400-49995000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:49989600-49989800	Weak transcription	Primary T cells from cord blood	blood
47	chr5:49989600-49991400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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