Variant report

Variant	rs2778498
Chromosome Location	chr6:24936645-24936646
allele	C/T
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	IKZF1	chr6:24935756-24936672	GM12878	blood:	n/a	n/a
4	FOXM1	chr6:24935864-24936696	GM12878	blood:	n/a	n/a
5	RUNX3	chr6:24935979-24937462	GM12878	blood:	n/a	n/a
6	MXI1	chr6:24935803-24937413	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:24935613-24937814	GM12878	blood:	n/a	n/a
8	CHD2	chr6:24936091-24937330	GM12878	blood:	n/a	n/a
9	EBF1	chr6:24935713-24937530	GM12878	blood:	n/a	chr6:24936312-24936323
10	RELA	chr6:24935759-24937419	GM12878	blood:	n/a	chr6:24937034-24937043 chr6:24937034-24937043
11	RELA	chr6:24935990-24937369	GM19193	blood:	n/a	chr6:24937034-24937043 chr6:24937034-24937043
12	BHLHE40	chr6:24935965-24937356	GM12878	blood:	n/a	n/a
13	TBL1XR1	chr6:24935576-24937746	GM12878	blood:	n/a	n/a
14	CEBPB	chr6:24936050-24937421	GM12878	blood:	n/a	chr6:24936807-24936820 chr6:24936807-24936818 chr6:24937234-24937245 chr6:24937232-24937245
15	POLR2A	chr6:24935585-24937550	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:24936566-24937660	GM12892	blood:	n/a	n/a
17	ATF2	chr6:24935954-24937420	GM12878	blood:	n/a	n/a
18	FOXM1	chr6:24935953-24937375	GM12878	blood:	n/a	n/a
19	NFIC	chr6:24935608-24937478	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:24935537-24937722	GM12891	blood:	n/a	n/a
21	MTA3	chr6:24935508-24937744	GM12878	blood:	n/a	n/a
22	STAT5A	chr6:24936412-24937404	GM12878	blood:	n/a	n/a
23	PML	chr6:24936560-24937407	GM12878	blood:	n/a	n/a
24	BCLAF1	chr6:24935923-24937456	GM12878	blood:	n/a	chr6:24937035-24937044 chr6:24937117-24937125
25	POLR2A	chr6:24935876-24937454	GM12892	blood:	n/a	n/a
26	EP300	chr6:24935831-24937344	GM12878	blood:	n/a	chr6:24935960-24935974 chr6:24936808-24936822 chr6:24937136-24937146 chr6:24937233-24937247
27	NFATC1	chr6:24936506-24937464	GM12878	blood:	n/a	n/a
28	CHD1	chr6:24935689-24937305	GM12878	blood:	n/a	n/a
29	MAZ	chr6:24936090-24937411	GM12878	blood:	n/a	n/a
30	EP300	chr6:24936121-24937499	GM12878	blood:	n/a	chr6:24936808-24936822 chr6:24937136-24937146 chr6:24937233-24937247
31	MTA3	chr6:24936523-24937599	GM12878	blood:	n/a	n/a
32	NFATC1	chr6:24935978-24937347	GM12878	blood:	n/a	n/a
33	ATF2	chr6:24936595-24937362	GM12878	blood:	n/a	n/a
34	JUND	chr6:24935983-24937388	GM12878	blood:	n/a	chr6:24936200-24936209 chr6:24937013-24937025 chr6:24936176-24936187
35	TBP	chr6:24935940-24937432	GM12878	blood:	n/a	n/a
36	CUX1	chr6:24936120-24937244	GM12878	blood:	n/a	n/a

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: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2747672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2778499	0.83[YRI][hapmap]
rs2778500	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2817745	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59512417	1.00[EUR][1000 genomes]
rs6904098	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6917505	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7758891	1.00[EUR][1000 genomes]
rs7769907	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	chr6:24931000-24936800	Weak transcription	Gastric	stomach
3	chr6:24931000-24937800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:24931200-24937200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:24932400-24937200	Active TSS	Primary T killer memory cells from peripheral blood	blood
6	chr6:24932600-24937200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:24932800-24936800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:24933600-24936800	Active TSS	Primary T cells fromperipheralblood	blood
9	chr6:24933600-24937400	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr6:24934200-24937200	Weak transcription	Spleen	Spleen
11	chr6:24934600-24936800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:24935200-24937000	Active TSS	Primary B cells from peripheral blood	blood
13	chr6:24935200-24937000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr6:24935600-24936800	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr6:24935600-24937000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:24935800-24936800	Flanking Active TSS	GM12878-XiMat	blood
17	chr6:24936000-24937400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:24936200-24936800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:24936200-24937000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:24936200-24937000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:24936200-24937000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr6:24936200-24937200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr6:24936200-24937200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr6:24936200-24937200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:24936200-24937200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr6:24936200-24937200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr6:24936200-24937400	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr6:24936200-24937400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:24936200-24937600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr6:24936200-24939000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr6:24936200-24941200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:24936400-24936800	Weak transcription	Brain Anterior Caudate	brain
33	chr6:24936400-24937200	Weak transcription	Thymus	Thymus
34	chr6:24936400-24937600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:24936400-24937600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:24936400-24937800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:24936400-24938000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr6:24936400-24938000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:24936400-24938200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr6:24936400-24938600	Enhancers	Fetal Thymus	thymus
41	chr6:24936400-24938800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr6:24936600-24936800	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr6:24936600-24936800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr6:24936600-24936800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:24936600-24936800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr6:24936600-24936800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:24936600-24937000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:24936600-24937000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr6:24936600-24937200	Enhancers	H9 Cell Line	embryonic stem cell
50	chr6:24936600-24937600	Enhancers	Dnd41	blood

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