Variant report

Variant	rs56999860
Chromosome Location	chr6:33260622-33260623
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	chr6:33257990-33262052	K562	blood:	n/a	n/a
2	POLR2A	chr6:33259486-33261986	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:33256261-33262240	K562	blood:	n/a	n/a
4	POLR2A	chr6:33260451-33260738	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr6:33258021-33261304	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:33256458-33262163	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr6:33256661-33261506	K562	blood:	n/a	n/a
8	POLR2A	chr6:33260574-33261516	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr6:33260251-33261656	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr6:33256842-33262829	K562	blood:	n/a	n/a
11	POLR2A	chr6:33256598-33261687	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:33260163-33261464	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33259755..33275794-chr6:33276314..33291745,68	MCF-7	breast:
2	chr6:33258827..33261135-chr6:33395874..33397870,2	K562	blood:

Variant related genes	Relation type
WDR46	TF binding region
ENSG00000204209	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000236104	Chromatin interaction

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

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

rs_ID	r²[population]
rs58283032	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58759132	0.81[AFR][1000 genomes]
rs58883992	0.80[AFR][1000 genomes]
rs59097151	0.80[AFR][1000 genomes]
rs59531270	0.81[AFR][1000 genomes]
rs60170976	0.80[AFR][1000 genomes]
rs73410003	0.82[AFR][1000 genomes]
rs73410010	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
3	esv3353999	chr6:33258174-33261772	Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33258200-33264800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:33258200-33265000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:33258200-33265200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:33258400-33261200	Strong transcription	Brain Angular Gyrus	brain
5	chr6:33258400-33264600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:33258400-33264800	Weak transcription	Stomach Mucosa	stomach
7	chr6:33258400-33265000	Weak transcription	Right Atrium	heart
8	chr6:33258600-33261800	Strong transcription	Stomach Smooth Muscle	stomach
9	chr6:33258600-33262000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:33258600-33263400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:33258600-33263800	Strong transcription	Fetal Thymus	thymus
12	chr6:33258600-33264400	Weak transcription	Fetal Heart	heart
13	chr6:33258600-33264400	Strong transcription	Fetal Intestine Large	intestine
14	chr6:33258600-33264600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:33258600-33264600	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr6:33258600-33264800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:33258600-33264800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:33258600-33264800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:33258600-33264800	Strong transcription	Brain Hippocampus Middle	brain
20	chr6:33258600-33264800	Strong transcription	Fetal Muscle Leg	muscle
21	chr6:33258600-33264800	Strong transcription	Lung	lung
22	chr6:33258600-33264800	Weak transcription	A549	lung
23	chr6:33258800-33260800	Strong transcription	Spleen	Spleen
24	chr6:33258800-33261600	Strong transcription	Placenta	Placenta
25	chr6:33258800-33262800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:33258800-33263600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:33258800-33263800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:33258800-33263800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr6:33258800-33263800	Strong transcription	Fetal Brain Female	brain
30	chr6:33258800-33264200	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr6:33258800-33264200	Strong transcription	Adipose Nuclei	Adipose
32	chr6:33258800-33264400	Strong transcription	Brain Cingulate Gyrus	brain
33	chr6:33258800-33264400	Strong transcription	Ovary	ovary
34	chr6:33258800-33264400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:33258800-33264400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr6:33258800-33264600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr6:33258800-33264600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:33258800-33264600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:33258800-33264600	Strong transcription	Brain Anterior Caudate	brain
40	chr6:33258800-33264600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:33258800-33264600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:33258800-33264600	Strong transcription	NHLF	lung
43	chr6:33258800-33264800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:33258800-33264800	Strong transcription	Primary B cells from cord blood	blood
45	chr6:33258800-33264800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr6:33258800-33264800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr6:33258800-33264800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr6:33258800-33264800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:33258800-33264800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr6:33259000-33260800	Strong transcription	Brain Substantia Nigra	brain

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