Variant report

Variant	rs56262509
Chromosome Location	chr6:5004253-5004254
allele	A/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	POLR2A	chr6:5003836-5004585	U87	brain:	n/a	n/a
2	ELK1	chr6:5004129-5004472	GM12878	blood:	n/a	n/a
3	PAX5	chr6:5003668-5004394	GM12892	blood:	n/a	n/a
4	TAF1	chr6:5003600-5004569	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr6:5004207-5004523	Spleen_OC	spleen:	n/a	chr6:5004341-5004350
6	POLR2A	chr6:5003644-5004827	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:5003688-5004557	HCT-116	colon:	n/a	n/a
8	TCF12	chr6:5003666-5004629	A549	lung:	n/a	n/a
9	MXI1	chr6:5003627-5004538	Hela-S3	cervix:	n/a	chr6:5003751-5003760
10	TAF1	chr6:5003999-5004612	K562	blood:	n/a	n/a
11	POLR2A	chr6:5003830-5004591	U87	brain:	n/a	n/a
12	MAZ	chr6:5003707-5004821	HepG2	liver:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
13	POLR2A	chr6:5004036-5004400	U87	brain:	n/a	n/a
14	EP300	chr6:5003642-5004866	HepG2	liver:	n/a	chr6:5003891-5003907 chr6:5004327-5004343 chr6:5003813-5003826
15	CTCF	chr6:5004220-5004370	HCM	heart:	n/a	chr6:5004341-5004350
16	RAD21	chr6:5003809-5004560	H1-hESC	embryonic stem cell:	n/a	n/a
17	HDAC2	chr6:5004030-5004444	K562	blood:	n/a	n/a
18	IRF1	chr6:5003726-5004893	K562	blood:	n/a	chr6:5004545-5004559
19	CTCF	chr6:5004001-5004702	K562	blood:	n/a	chr6:5004341-5004350
20	CTCF	chr6:5004111-5004543	K562	blood:	n/a	chr6:5004341-5004350
21	POLR2A	chr6:5004018-5004579	GM12878	blood:	n/a	n/a
22	EP300	chr6:5003760-5004789	GM12878	blood:	n/a	chr6:5003891-5003907 chr6:5004327-5004343 chr6:5003813-5003826
23	MAX	chr6:5003525-5004607	ECC-1	luminal epithelium:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
24	MYC	chr6:5003609-5004827	K562	blood:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
25	CEBPD	chr6:5003832-5004332	K562	blood:	n/a	n/a
26	CUX1	chr6:5003914-5005064	K562	blood:	n/a	n/a
27	PAX5	chr6:5003745-5004466	GM12878	blood:	n/a	n/a
28	YY1	chr6:5003855-5004606	SK-N-SH	brain:	n/a	n/a
29	TEAD4	chr6:5003761-5004546	K562	blood:	n/a	n/a
30	POLR2A	chr6:5003616-5004747	GM18951	blood:	n/a	n/a
31	CTCF	chr6:5003503-5005179	A549	lung:	n/a	chr6:5004341-5004350
32	CTBP2	chr6:5003730-5004643	H1-hESC	embryonic stem cell:	n/a	n/a
33	TEAD4	chr6:5003707-5004566	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr6:5003628-5004534	Hela-S3	cervix:	n/a	n/a
35	ETS1	chr6:5003667-5004559	GM12878	blood:	n/a	chr6:5003970-5003977 chr6:5003914-5003927 chr6:5003915-5003928 chr6:5003916-5003923 chr6:5003966-5003979 chr6:5004344-5004355 chr6:5003965-5003978
36	HCFC1	chr6:5003522-5005044	Hela-S3	cervix:	n/a	n/a
37	MAX	chr6:5003592-5004610	SK-N-SH	brain:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
38	MAX	chr6:5003546-5004563	H1-hESC	embryonic stem cell:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
39	POLR2A	chr6:5003637-5004559	A549	lung:	n/a	n/a
40	RELA	chr6:5003654-5004947	GM15510	blood:	n/a	n/a
41	RELA	chr6:5003697-5005152	GM18505	blood:	n/a	n/a
42	JUN	chr6:5003758-5004404	K562	blood:	n/a	n/a
43	MYC	chr6:5003621-5004404	H1-hESC	embryonic stem cell:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
44	POLR2A	chr6:5003576-5004546	Hela-S3	cervix:	n/a	n/a
45	HEY1	chr6:5003604-5004640	K562	blood:	n/a	chr6:5004338-5004353
46	EP300	chr6:5004226-5004810	HepG2	liver:	n/a	chr6:5004327-5004343
47	POLR2A	chr6:5003622-5004760	K562	blood:	n/a	n/a
48	SIN3AK20	chr6:5003692-5004462	PFSK-1	brain:	n/a	n/a
49	CTCF	chr6:5004191-5004502	GM12891	blood:	n/a	chr6:5004341-5004350
50	BHLHE40	chr6:5003751-5004507	GM12878	blood:	n/a	chr6:5004328-5004344

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4776139..4778956-chr6:5002447..5004557,2	K562	blood:
2	chr6:5002773..5004480-chr6:5029318..5032794,4	MCF-7	breast:

Variant related genes	Relation type
RPP40	TF binding region
ENSG00000153046	Chromatin interaction
ENSG00000272142	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs61033666	1.00[AFR][1000 genomes]
rs73717619	0.83[AFR][1000 genomes]
rs73717799	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5003000-5004600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr6:5003000-5004800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:5003000-5005000	Active TSS	Brain Anterior Caudate	brain
4	chr6:5003200-5004400	Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr6:5003200-5004400	Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr6:5003200-5004400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:5003200-5004600	Active TSS	Brain Hippocampus Middle	brain
8	chr6:5003200-5004600	Active TSS	Duodenum Mucosa	Duodenum
9	chr6:5003200-5004600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
10	chr6:5003200-5004600	Active TSS	Hela-S3	cervix
11	chr6:5003200-5004600	Active TSS	Osteobl	bone
12	chr6:5003200-5004800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:5003200-5004800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr6:5003200-5004800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:5003200-5004800	Active TSS	NHDF-Ad	bronchial
16	chr6:5003200-5004800	Active TSS	NHEK	skin
17	chr6:5003200-5005000	Active TSS	A549	lung
18	chr6:5003200-5005200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr6:5003200-5005200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:5003400-5004400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr6:5003400-5004400	Active TSS	Muscle Satellite Cultured Cells	--
22	chr6:5003400-5004400	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr6:5003400-5004400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:5003400-5004400	Active TSS	Colonic Mucosa	Colon
25	chr6:5003400-5004600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:5003400-5004600	Active TSS	Fetal Brain Female	brain
27	chr6:5003400-5004600	Active TSS	Fetal Intestine Large	intestine
28	chr6:5003400-5004600	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr6:5003400-5004600	Active TSS	GM12878-XiMat	blood
30	chr6:5003400-5004600	Active TSS	NH-A	brain
31	chr6:5003400-5004800	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr6:5003400-5004800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:5003400-5004800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:5003400-5004800	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr6:5003400-5004800	Active TSS	HSMM	muscle
36	chr6:5003400-5005200	Active TSS	Psoas Muscle	Psoas
37	chr6:5003600-5004400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr6:5003600-5004400	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr6:5003600-5004400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:5003600-5004400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:5003600-5004400	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr6:5003600-5004600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:5003600-5004600	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr6:5003600-5004600	Active TSS	Primary T cells from cord blood	blood
45	chr6:5003600-5004600	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr6:5003600-5004600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:5003600-5004600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr6:5003600-5004600	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr6:5003600-5004600	Active TSS	Brain Angular Gyrus	brain
50	chr6:5003600-5004600	Active TSS	Brain Inferior Temporal Lobe	brain

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