Variant report

Variant	rs549958736
Chromosome Location	chr6:29690626-29690627
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	ZNF263	chr6:29690368-29691781	HEK293-T-REx	kidney:	n/a	chr6:29690503-29690524 chr6:29690535-29690556 chr6:29690559-29690580
2	RFX5	chr6:29690604-29692339	H1-hESC	embryonic stem cell:	n/a	n/a
3	STAT5A	chr6:29690608-29692291	GM12878	blood:	n/a	n/a
4	MTA3	chr6:29690560-29692415	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:29690575-29695009	GM12878	blood:	n/a	n/a
6	EBF1	chr6:29690575-29692170	GM12878	blood:	n/a	chr6:29690978-29690989
7	POLR2A	chr6:29690566-29699452	GM12892	blood:	n/a	n/a
8	POLR2A	chr6:29690622-29694243	GM12891	blood:	n/a	n/a
9	POLR2A	chr6:29690618-29699456	GM12892	blood:	n/a	n/a
10	POLR2A	chr6:29690594-29697494	GM12878	blood:	n/a	n/a
11	MTA3	chr6:29690619-29691038	GM12878	blood:	n/a	n/a
12	PML	chr6:29690553-29692088	GM12878	blood:	n/a	n/a
13	CREB1	chr6:29690590-29692094	GM12878	blood:	n/a	n/a
14	RFX5	chr6:29690415-29692037	SK-N-SH	brain:	n/a	n/a
15	RFX5	chr6:29690479-29691959	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29689319..29693460-chr6:29694038..29698697,5	MCF-7	breast:
2	chr6:29689852..29692667-chr6:31324164..31326641,2	K562	blood:

Variant related genes	Relation type
HLA-F	TF binding region
ENSG00000234745	Chromatin interaction
ENSG00000271581	Chromatin interaction
ENSG00000239257	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv970675	chr6:29657036-29692268	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv462673	chr6:29689590-29700183	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv601230	chr6:29689590-29700183	Flanking Active TSS Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv2291610	chr6:29690346-29690843	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv3499644	chr6:29690412-29690732	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	esv3323076	chr6:29690413-29690750	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	esv3499645	chr6:29690414-29690762	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv3472346	chr6:29690437-29690698	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	esv3472347	chr6:29690437-29690698	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	esv3836	chr6:29690467-29690736	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	esv3347174	chr6:29690514-29690721	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29688600-29690800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:29689400-29690800	Weak transcription	Spleen	Spleen
3	chr6:29690000-29691200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr6:29690000-29692000	Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr6:29690000-29692000	Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr6:29690000-29692200	Active TSS	GM12878-XiMat	blood
7	chr6:29690200-29690800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr6:29690200-29691200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr6:29690200-29692000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr6:29690400-29690800	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr6:29690400-29691000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:29690400-29691200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:29690400-29691800	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
14	chr6:29690400-29692000	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr6:29690400-29692000	Active TSS	Primary T cells fromperipheralblood	blood
16	chr6:29690400-29692000	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr6:29690400-29692000	Active TSS	Brain Anterior Caudate	brain
18	chr6:29690400-29692000	Active TSS	Duodenum Mucosa	Duodenum
19	chr6:29690400-29692600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr6:29690400-29692800	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr6:29690600-29690800	Active TSS	Primary hematopoietic stem cells	blood
22	chr6:29690600-29690800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:29690600-29690800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:29690600-29690800	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr6:29690600-29690800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
26	chr6:29690600-29690800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
27	chr6:29690600-29690800	Bivalent Enhancer	Fetal Thymus	thymus
28	chr6:29690600-29690800	Bivalent Enhancer	HepG2	liver
29	chr6:29690600-29690800	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
30	chr6:29690600-29691000	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr6:29690600-29691000	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:29690600-29691000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
33	chr6:29690600-29691000	Active TSS	Psoas Muscle	Psoas
34	chr6:29690600-29691000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
35	chr6:29690600-29691000	Flanking Active TSS	Thymus	Thymus
36	chr6:29690600-29691000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr6:29690600-29691000	Flanking Active TSS	NHEK	skin
38	chr6:29690600-29691200	Active TSS	Muscle Satellite Cultured Cells	--
39	chr6:29690600-29691200	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:29690600-29691200	Bivalent/Poised TSS	Placenta	Placenta
41	chr6:29690600-29691200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
42	chr6:29690600-29691200	Active TSS	NH-A	brain
43	chr6:29690600-29691400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:29690600-29691400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:29690600-29691400	Active TSS	Colonic Mucosa	Colon
46	chr6:29690600-29691400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
47	chr6:29690600-29691400	Active TSS	Right Ventricle	heart
48	chr6:29690600-29691400	Active TSS	HMEC	breast
49	chr6:29690600-29691400	Active TSS	NHLF	lung
50	chr6:29690600-29691600	Active TSS	Brain Inferior Temporal Lobe	brain

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