Variant report

Variant	rs6869017
Chromosome Location	chr5:118668538-118668539
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr5:118668154-118668654	K562	blood:	n/a	n/a
2	ATF2	chr5:118667855-118669525	GM12878	blood:	n/a	n/a
3	NFIC	chr5:118668441-118669774	GM12878	blood:	n/a	n/a
4	RUNX3	chr5:118668174-118669306	GM12878	blood:	n/a	n/a
5	MYC	chr5:118668413-118669373	MCF10A-Er-Src	breast:	n/a	n/a
6	ZNF384	chr5:118668040-118669352	GM12878	blood:	n/a	n/a
7	MTA3	chr5:118667887-118669619	GM12878	blood:	n/a	n/a
8	FOXM1	chr5:118668442-118669581	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:118668312-118669781	GM18505	blood:	n/a	n/a
10	POLR2A	chr5:118667999-118669856	GM12891	blood:	n/a	n/a
11	PML	chr5:118667769-118669514	GM12878	blood:	n/a	n/a
12	NFIC	chr5:118668396-118669282	GM12878	blood:	n/a	n/a
13	EBF1	chr5:118668442-118669730	GM12878	blood:	n/a	n/a
14	MXI1	chr5:118668520-118669713	GM12878	blood:	n/a	n/a
15	FOS	chr5:118668401-118669668	MCF10A-Er-Src	breast:	n/a	chr5:118669073-118669085 chr5:118669422-118669431 chr5:118668578-118668590
16	TBL1XR1	chr5:118668360-118668541	K562	blood:	n/a	n/a
17	BCLAF1	chr5:118668446-118669754	GM12878	blood:	n/a	n/a
18	IKZF1	chr5:118668390-118669148	GM12878	blood:	n/a	n/a
19	GATA1	chr5:118665615-118668722	K562	blood:	n/a	chr5:118666137-118666154 chr5:118666483-118666492 chr5:118667718-118667739 chr5:118666485-118666492 chr5:118666097-118666109
20	MTA3	chr5:118668187-118669411	GM12878	blood:	n/a	n/a
21	FOS	chr5:118668508-118668878	MCF10A-Er-Src	breast:	n/a	chr5:118668578-118668590
22	TBL1XR1	chr5:118668475-118669777	GM12878	blood:	n/a	n/a
23	FOS	chr5:118668488-118669629	MCF10A-Er-Src	breast:	n/a	chr5:118669073-118669085 chr5:118669422-118669431 chr5:118668578-118668590
24	STAT3	chr5:118668417-118669564	MCF10A-Er-Src	breast:	n/a	chr5:118668852-118668859 chr5:118669417-118669428
25	MEF2A	chr5:118668415-118669097	GM12878	blood:	n/a	chr5:118668696-118668711 chr5:118668695-118668711 chr5:118668696-118668712
26	CHD1	chr5:118668396-118669742	GM12878	blood:	n/a	n/a
27	POLR2A	chr5:118668322-118671087	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:118623648..118626074-chr5:118666762..118668589,2	MCF-7	breast:
2	chr5:118668038..118668652-chr5:118747446..118748001,2	MCF-7	breast:
3	chr5:118666728..118668661-chr5:118669320..118670898,2	MCF-7	breast:
4	chr5:118405258..118407472-chr5:118664950..118669105,3	K562	blood:

Variant related genes	Relation type
TNFAIP8	TF binding region
ENSG00000172869	Chromatin interaction
ENSG00000249494	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11950366	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951771	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11954854	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955852	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956042	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956215	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11956285	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11958957	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11959451	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11959659	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11959729	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11959964	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960246	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960654	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17145189	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17145194	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17145196	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17145198	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17164572	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876737	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813301	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813302	0.95[ASN][1000 genomes]
rs3813304	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813305	0.84[EUR][1000 genomes]
rs4392658	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60161062	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60507834	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60756572	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66535134	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67154545	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67311526	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67708265	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6861849	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862299	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862320	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862517	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862831	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868688	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868702	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875361	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883394	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786136	0.98[EUR][1000 genomes]
rs72786141	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786142	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786143	0.98[EUR][1000 genomes]
rs72786144	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786149	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786152	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786157	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786159	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786161	0.98[EUR][1000 genomes]
rs73235259	0.89[ASN][1000 genomes]
rs73235260	0.89[ASN][1000 genomes]
rs73790807	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703577	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703998	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704026	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704291	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704326	0.89[ASN][1000 genomes]
rs7704334	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704386	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704398	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704487	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7707221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7707736	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710939	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711101	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7711312	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712227	0.98[EUR][1000 genomes]
rs7721976	0.89[ASN][1000 genomes]
rs7722687	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7722699	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7723976	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724082	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724178	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724204	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725244	0.98[EUR][1000 genomes]
rs7725878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737934	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024648	chr5:118608175-118678268	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv869828	chr5:118610548-118691190	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv599565	chr5:118661882-118691888	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118658200-118670400	Weak transcription	Lung	lung
2	chr5:118659600-118677800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:118660200-118675600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr5:118660200-118678600	Weak transcription	HepG2	liver
5	chr5:118660400-118668600	Enhancers	Primary hematopoietic stem cells	blood
6	chr5:118660400-118670400	Weak transcription	Right Atrium	heart
7	chr5:118662600-118669000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:118662600-118670400	Weak transcription	Right Ventricle	heart
9	chr5:118662800-118668800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr5:118663000-118669600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr5:118663600-118668600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:118663800-118669200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr5:118664000-118668800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:118664200-118671600	Weak transcription	Small Intestine	intestine
15	chr5:118664200-118673400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr5:118664400-118678200	Weak transcription	Fetal Kidney	kidney
17	chr5:118664600-118669200	Enhancers	Colonic Mucosa	Colon
18	chr5:118664800-118668800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:118664800-118670600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:118664800-118673000	Weak transcription	HSMM	muscle
21	chr5:118665000-118670400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:118665000-118670600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:118665000-118672600	Weak transcription	Hela-S3	cervix
24	chr5:118665200-118669200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:118665200-118670400	Weak transcription	Osteobl	bone
26	chr5:118665400-118670600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:118665400-118670600	Weak transcription	NHLF	lung
28	chr5:118665400-118677000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:118665600-118670000	Genic enhancers	Dnd41	blood
30	chr5:118665600-118670400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr5:118665600-118670400	Weak transcription	Aorta	Aorta
32	chr5:118665600-118670600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr5:118665800-118668800	Enhancers	Primary B cells from peripheral blood	blood
34	chr5:118665800-118668800	Enhancers	Thymus	Thymus
35	chr5:118665800-118669000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr5:118665800-118670600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr5:118665800-118672600	Weak transcription	Fetal Intestine Small	intestine
38	chr5:118665800-118673200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:118666000-118668600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr5:118666200-118669400	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr5:118666200-118672200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:118666400-118669000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr5:118666400-118669600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr5:118666600-118668800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:118666600-118670400	Weak transcription	Adipose Nuclei	Adipose
46	chr5:118666600-118672600	Weak transcription	Fetal Stomach	stomach
47	chr5:118666800-118668600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr5:118666800-118669000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr5:118666800-118671000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr5:118667000-118668800	Enhancers	Fetal Thymus	thymus

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