Variant report

Variant	rs16889798
Chromosome Location	chr6:24936923-24936924
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	NFIC	chr6:24935794-24937440	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:24935562-24938197	GM18505	blood:	n/a	n/a
3	POU2F2	chr6:24936836-24937316	GM12878	blood:	n/a	chr6:24937089-24937102 chr6:24937095-24937104 chr6:24937096-24937103 chr6:24937093-24937104
4	FOXM1	chr6:24936743-24937514	GM12878	blood:	n/a	n/a
5	RUNX3	chr6:24935979-24937462	GM12878	blood:	n/a	n/a
6	RELA	chr6:24936746-24937530	GM18505	blood:	n/a	chr6:24937034-24937043 chr6:24937034-24937043
7	CEBPB	chr6:24936758-24936946	A549	lung:	n/a	chr6:24936807-24936820 chr6:24936807-24936818
8	POLR2A	chr6:24936703-24937480	GM12891	blood:	n/a	n/a
9	MXI1	chr6:24935803-24937413	GM12878	blood:	n/a	n/a
10	CEBPB	chr6:24936684-24937184	IMR90	lung:	n/a	chr6:24936807-24936820 chr6:24936807-24936818
11	TAF1	chr6:24936809-24937237	GM12878	blood:	n/a	n/a
12	SP1	chr6:24936736-24937344	GM12878	blood:	n/a	n/a
13	YY1	chr6:24936785-24937385	GM12892	blood:	n/a	n/a
14	SMC3	chr6:24936882-24937447	GM12878	blood:	n/a	n/a
15	STAT3	chr6:24936860-24937151	MCF10A-Er-Src	breast:	n/a	n/a
16	RELA	chr6:24936782-24937422	GM18951	blood:	n/a	chr6:24937034-24937043 chr6:24937034-24937043
17	POLR2A	chr6:24935613-24937814	GM12878	blood:	n/a	n/a
18	CHD2	chr6:24936091-24937330	GM12878	blood:	n/a	n/a
19	YY1	chr6:24936833-24937424	GM12878	blood:	n/a	n/a
20	EBF1	chr6:24935713-24937530	GM12878	blood:	n/a	chr6:24936312-24936323
21	EBF1	chr6:24936680-24937250	GM12878	blood:	n/a	n/a
22	E2F4	chr6:24936749-24936949	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr6:24936715-24937198	GM12891	blood:	n/a	n/a
24	BCL3	chr6:24936740-24937249	GM12878	blood:	n/a	chr6:24937035-24937044 chr6:24937117-24937125
25	SP1	chr6:24936809-24937317	GM12878	blood:	n/a	n/a
26	STAT3	chr6:24936906-24937210	MCF10A-Er-Src	breast:	n/a	n/a
27	BCL11A	chr6:24936798-24937346	GM12878	blood:	n/a	chr6:24937035-24937044 chr6:24937117-24937125
28	RELA	chr6:24936742-24937740	GM15510	blood:	n/a	chr6:24937034-24937043 chr6:24937034-24937043
29	NFYB	chr6:24936757-24937195	GM12878	blood:	n/a	n/a
30	BATF	chr6:24936757-24937242	GM12878	blood:	n/a	n/a
31	EBF1	chr6:24936729-24937171	GM12878	blood:	n/a	n/a
32	YY1	chr6:24936777-24937265	GM12878	blood:	n/a	n/a
33	TAF1	chr6:24936865-24937134	GM12892	blood:	n/a	n/a
34	RELA	chr6:24935759-24937419	GM12878	blood:	n/a	chr6:24937034-24937043 chr6:24937034-24937043
35	RELA	chr6:24935990-24937369	GM19193	blood:	n/a	chr6:24937034-24937043 chr6:24937034-24937043
36	MEF2C	chr6:24936775-24937459	GM12878	blood:	n/a	chr6:24937136-24937151 chr6:24937134-24937155 chr6:24937134-24937155 chr6:24937136-24937150
37	BHLHE40	chr6:24935965-24937356	GM12878	blood:	n/a	n/a
38	BATF	chr6:24936765-24937308	GM12878	blood:	n/a	n/a
39	MEF2A	chr6:24936673-24937449	GM12878	blood:	n/a	chr6:24937134-24937155 chr6:24937134-24937155 chr6:24937136-24937150
40	MAX	chr6:24936803-24937386	GM12878	blood:	n/a	n/a
41	TBL1XR1	chr6:24935576-24937746	GM12878	blood:	n/a	n/a
42	CEBPB	chr6:24936050-24937421	GM12878	blood:	n/a	chr6:24936807-24936820 chr6:24936807-24936818 chr6:24937234-24937245 chr6:24937232-24937245
43	POLR2A	chr6:24935585-24937550	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:24936566-24937660	GM12892	blood:	n/a	n/a
45	ATF2	chr6:24935954-24937420	GM12878	blood:	n/a	n/a
46	FOXM1	chr6:24935953-24937375	GM12878	blood:	n/a	n/a
47	MYC	chr6:24936817-24937126	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr6:24936835-24937046	GM12878	blood:	n/a	n/a
49	FOS	chr6:24936790-24937217	MCF10A-Er-Src	breast:	n/a	chr6:24937013-24937025
50	POU2F2	chr6:24936777-24937323	GM12891	blood:	n/a	chr6:24937089-24937102 chr6:24937095-24937104 chr6:24937096-24937103 chr6:24937093-24937104

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24929367..24931167-chr6:24936238..24937978,2	MCF-7	breast:

Variant related genes	Relation type
FAM65B	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10946736	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760083	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410684	0.81[ASN][1000 genomes]
rs587009	0.89[CHB][hapmap]
rs6929465	0.88[CHB][hapmap]
rs9461082	0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs9467355	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24930800-24938200	Weak transcription	Right Atrium	heart
2	chr6:24931000-24937800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:24931200-24937200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:24932400-24937200	Active TSS	Primary T killer memory cells from peripheral blood	blood
5	chr6:24932600-24937200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:24933600-24937400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:24934200-24937200	Weak transcription	Spleen	Spleen
8	chr6:24935200-24937000	Active TSS	Primary B cells from peripheral blood	blood
9	chr6:24935200-24937000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr6:24935600-24937000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr6:24936000-24937400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:24936200-24937000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:24936200-24937000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:24936200-24937000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr6:24936200-24937200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:24936200-24937200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr6:24936200-24937200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:24936200-24937200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:24936200-24937200	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr6:24936200-24937400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:24936200-24937400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:24936200-24937600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr6:24936200-24939000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr6:24936200-24941200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:24936400-24937200	Weak transcription	Thymus	Thymus
26	chr6:24936400-24937600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:24936400-24937600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:24936400-24937800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:24936400-24938000	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr6:24936400-24938000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:24936400-24938200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr6:24936400-24938600	Enhancers	Fetal Thymus	thymus
33	chr6:24936400-24938800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr6:24936600-24937000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:24936600-24937000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr6:24936600-24937200	Enhancers	H9 Cell Line	embryonic stem cell
37	chr6:24936600-24937600	Enhancers	Dnd41	blood
38	chr6:24936800-24937000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:24936800-24937000	Active TSS	Primary T cells from cord blood	blood
40	chr6:24936800-24937000	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr6:24936800-24937000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:24936800-24937200	Enhancers	Brain Anterior Caudate	brain
43	chr6:24936800-24937200	Active TSS	GM12878-XiMat	blood
44	chr6:24936800-24937400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:24936800-24937400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
46	chr6:24936800-24937400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:24936800-24937400	Enhancers	Gastric	stomach
48	chr6:24936800-24937600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:24936800-24937800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr6:24936800-24938000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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