Variant report

Variant	rs9504249
Chromosome Location	chr6:4778629-4778630
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	RELA	chr6:4777462-4778900	GM12878	blood:	n/a	n/a
2	RELA	chr6:4777389-4778895	GM18951	blood:	n/a	n/a
3	ATF2	chr6:4778161-4778898	GM12878	blood:	n/a	n/a
4	STAT3	chr6:4778345-4778851	GM12878	blood:	n/a	chr6:4778684-4778695
5	CEBPB	chr6:4778412-4778776	A549	lung:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
6	RCOR1	chr6:4778325-4778807	GM12878	blood:	n/a	n/a
7	EP300	chr6:4778345-4778703	GM12878	blood:	n/a	n/a
8	STAT5A	chr6:4778064-4778852	GM12878	blood:	n/a	chr6:4778684-4778695
9	POLR2A	chr6:4777394-4778648	GM12891	blood:	n/a	n/a
10	CREB1	chr6:4778167-4778918	GM12878	blood:	n/a	n/a
11	RFX5	chr6:4778340-4778674	GM12878	blood:	n/a	n/a
12	CUX1	chr6:4778432-4779173	GM12878	blood:	n/a	n/a
13	CBX3	chr6:4778271-4778844	HCT-116	colon:	n/a	n/a
14	NFATC1	chr6:4778028-4779019	GM12878	blood:	n/a	n/a
15	FOXM1	chr6:4778155-4778867	GM12878	blood:	n/a	n/a
16	ATF2	chr6:4778124-4778824	GM12878	blood:	n/a	n/a
17	CBX3	chr6:4778104-4778750	K562	blood:	n/a	n/a
18	SETDB1	chr6:4778111-4778964	U2OS	brain:	n/a	n/a
19	NFIC	chr6:4778165-4778686	GM12878	blood:	n/a	n/a
20	TBL1XR1	chr6:4778142-4778972	GM12878	blood:	n/a	n/a
21	BHLHE40	chr6:4777336-4778808	GM12878	blood:	n/a	n/a
22	KAP1	chr6:4777817-4779068	K562	blood:	n/a	n/a
23	KAP1	chr6:4777767-4778872	HEK293	kidney:	n/a	n/a
24	CEBPB	chr6:4778393-4778711	HepG2	liver:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
25	FOS	chr6:4778373-4778683	MCF10A-Er-Src	breast:	n/a	n/a
26	MTA3	chr6:4778058-4778837	GM12878	blood:	n/a	n/a
27	BCLAF1	chr6:4778228-4778689	GM12878	blood:	n/a	n/a
28	CEBPB	chr6:4778367-4778722	K562	blood:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
29	CBX3	chr6:4778236-4778740	K562	blood:	n/a	n/a
30	PML	chr6:4778009-4778800	GM12878	blood:	n/a	n/a
31	EBF1	chr6:4778134-4778757	GM12878	blood:	n/a	n/a
32	CEBPB	chr6:4778331-4778751	Hela-S3	cervix:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
33	CEBPB	chr6:4778387-4778689	IMR90	lung:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
34	CREB1	chr6:4778225-4778813	GM12878	blood:	n/a	n/a
35	TBP	chr6:4777392-4779043	GM12878	blood:	n/a	n/a
36	CEBPB	chr6:4777403-4778870	GM12878	blood:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
37	EP300	chr6:4778186-4778765	GM12878	blood:	n/a	n/a
38	MTA3	chr6:4778155-4778738	GM12878	blood:	n/a	n/a
39	RELA	chr6:4777413-4778869	GM19193	blood:	n/a	n/a
40	IKZF1	chr6:4778253-4778896	GM12878	blood:	n/a	n/a
41	EP300	chr6:4778379-4778669	Hela-S3	cervix:	n/a	n/a
42	ZNF143	chr6:4778029-4778970	GM12878	blood:	n/a	n/a
43	FOS	chr6:4778386-4778680	MCF10A-Er-Src	breast:	n/a	n/a
44	NFIC	chr6:4777359-4779165	GM12878	blood:	n/a	n/a
45	MXI1	chr6:4775628-4778903	SK-N-SH	brain:	n/a	chr6:4776030-4776039
46	RUNX3	chr6:4777284-4778919	GM12878	blood:	n/a	n/a
47	POLR2A	chr6:4776093-4778983	GM12878	blood:	n/a	n/a
48	NFATC1	chr6:4778269-4779212	GM12878	blood:	n/a	n/a
49	MYC	chr6:4778391-4778632	MCF10A-Er-Src	breast:	n/a	n/a
50	KAP1	chr6:4778005-4778800	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:4775417..4779410-chr6:4834974..4837006,3	MCF-7	breast:
2	chr6:4773447..4776687-chr6:4777915..4782551,4	MCF-7	breast:
3	chr6:4776139..4778956-chr6:5002447..5004557,2	K562	blood:
4	chr6:4488845..4492110-chr6:4777740..4781440,3	MCF-7	breast:
5	chr6:4775727..4780301-chr6:4925378..4930668,5	K562	blood:
6	chr6:4778081..4781516-chr6:4787216..4791667,5	MCF-7	breast:
7	chr6:4777710..4780092-chr6:4801744..4804702,2	K562	blood:

Variant related genes	Relation type
ENSG00000236336	TF binding region
ENSG00000124787	Chromatin interaction
ENSG00000153046	Chromatin interaction
ENSG00000236336	Chromatin interaction
ENSG00000260239	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13362643	1.00[EUR][1000 genomes]
rs6901998	1.00[EUR][1000 genomes]
rs73360653	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9504239	0.95[AFR][1000 genomes]
rs9504241	0.95[AFR][1000 genomes]
rs9504243	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9504246	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9504250	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3429586	chr6:4719363-4792438	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4775800-4778800	Active TSS	GM12878-XiMat	blood
2	chr6:4775800-4778800	Active TSS	NHLF	lung
3	chr6:4777800-4780200	Weak transcription	Gastric	stomach
4	chr6:4777800-4783600	Weak transcription	Lung	lung
5	chr6:4777800-4789000	Weak transcription	Pancreas	Pancrea
6	chr6:4778000-4779800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:4778000-4780400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr6:4778000-4782400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:4778200-4778800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:4778200-4778800	ZNF genes & repeats	NHDF-Ad	bronchial
11	chr6:4778200-4779400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:4778200-4780000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:4778200-4780000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr6:4778200-4780200	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:4778200-4780200	Weak transcription	Ovary	ovary
16	chr6:4778200-4781000	Weak transcription	Osteobl	bone
17	chr6:4778200-4781400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:4778200-4781600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:4778200-4785000	Weak transcription	Psoas Muscle	Psoas
20	chr6:4778200-4787000	Weak transcription	Thymus	Thymus
21	chr6:4778400-4778800	Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr6:4778400-4778800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:4778400-4778800	Active TSS	Fetal Heart	heart
24	chr6:4778400-4779000	ZNF genes & repeats	HepG2	liver
25	chr6:4778400-4779200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:4778400-4779400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:4778400-4779400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:4778400-4779400	ZNF genes & repeats	A549	lung
29	chr6:4778400-4779600	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:4778400-4780200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr6:4778400-4780200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:4778400-4780400	Weak transcription	Small Intestine	intestine
33	chr6:4778400-4780800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:4778400-4780800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:4778400-4780800	Weak transcription	Brain Angular Gyrus	brain
36	chr6:4778400-4780800	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:4778400-4781000	Weak transcription	Fetal Kidney	kidney
38	chr6:4778400-4781200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:4778400-4781200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:4778400-4781400	Weak transcription	Brain Substantia Nigra	brain
41	chr6:4778400-4781400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:4778400-4781400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:4778400-4781400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:4778400-4781400	Weak transcription	Right Ventricle	heart
45	chr6:4778400-4782000	Weak transcription	Placenta	Placenta
46	chr6:4778400-4782200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:4778400-4782400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr6:4778400-4782600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:4778400-4783000	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr6:4778400-4785000	Weak transcription	Left Ventricle	heart

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