Variant report

Variant	rs554209486
Chromosome Location	chr6:33387411-33387412
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr6:33384157-33388027	K562	blood:	n/a	chr6:33387272-33387283 chr6:33386177-33386186 chr6:33386981-33386990 chr6:33386847-33386856
2	MAZ	chr6:33387360-33389235	IMR90	lung:	n/a	chr6:33388927-33388937
3	MTA3	chr6:33383820-33387438	GM12878	blood:	n/a	n/a
4	REST	chr6:33387196-33388764	H1-neurons	neurons:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33242365..33247657-chr6:33386109..33388284,6	K562	blood:
2	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
3	chr6:33385453..33389637-chr6:33419628..33424957,5	MCF-7	breast:
4	chr6:33168527..33171468-chr6:33384494..33387586,3	K562	blood:
5	chr6:33254516..33257651-chr6:33384634..33387572,3	K562	blood:
6	chr6:33365854..33369434-chr6:33385468..33388336,3	K562	blood:
7	chr6:33264378..33268881-chr6:33383627..33388443,14	K562	blood:
8	chr6:33357638..33360083-chr6:33386720..33388943,3	MCF-7	breast:
9	chr6:33280795..33292485-chr6:33374786..33387605,31	K562	blood:
10	chr6:33356382..33361019-chr6:33384058..33388661,8	K562	blood:
11	chr6:33285422..33287849-chr6:33385883..33388858,2	MCF-7	breast:
12	chr6:33264858..33266557-chr6:33385922..33387524,2	K562	blood:
13	chr6:33237639..33241732-chr6:33383253..33390116,11	K562	blood:
14	chr6:33357335..33362175-chr6:33383352..33389421,14	K562	blood:
15	chr6:33242542..33249529-chr6:33381747..33388277,18	K562	blood:
16	chr6:33279097..33283546-chr6:33386045..33390564,5	MCF-7	breast:
17	chr6:33371627..33375942-chr6:33381284..33387543,6	K562	blood:
18	chr6:33237802..33241730-chr6:33382199..33389112,10	K562	blood:

No data

Variant related genes	Relation type
SYNGAP1	TF binding region
CUTA	TF binding region
ENSG00000227057	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000225644	Chromatin interaction
ENSG00000204194	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000213588	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv932196	chr6:33383131-33400706	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
6	esv3491403	chr6:33386574-33390272	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
7	esv3491404	chr6:33386574-33390272	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	esv3325690	chr6:33386999-33389547	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
9	esv3404776	chr6:33387074-33389997	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33386000-33387800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:33386000-33392600	Weak transcription	Gastric	stomach
3	chr6:33386200-33387800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:33386200-33387800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:33386200-33387800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:33386200-33387800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:33386200-33387800	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr6:33386200-33387800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:33386200-33387800	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr6:33386200-33387800	Flanking Active TSS	K562	blood
11	chr6:33386200-33388000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:33386200-33388000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:33386200-33389400	Flanking Active TSS	Dnd41	blood
14	chr6:33386400-33387600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:33386400-33387600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr6:33386400-33387600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr6:33386400-33387800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr6:33386400-33387800	Flanking Active TSS	Rectal Smooth Muscle	rectum
19	chr6:33386600-33387600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:33386600-33387600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:33386600-33387600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr6:33386600-33387600	Weak transcription	Aorta	Aorta
23	chr6:33386600-33387600	Enhancers	Fetal Intestine Large	intestine
24	chr6:33386600-33387600	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr6:33386600-33387600	Enhancers	Fetal Lung	lung
26	chr6:33386600-33387600	Enhancers	Fetal Muscle Trunk	muscle
27	chr6:33386600-33387600	Weak transcription	Ovary	ovary
28	chr6:33386600-33387600	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr6:33386600-33387800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:33386600-33387800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr6:33386600-33387800	Enhancers	Stomach Mucosa	stomach
32	chr6:33386600-33388000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:33386600-33388000	Enhancers	HMEC	breast
34	chr6:33386600-33388400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:33386600-33389200	Enhancers	Fetal Heart	heart
36	chr6:33386800-33387600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:33386800-33387600	Enhancers	Primary hematopoietic stem cells	blood
38	chr6:33386800-33387600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr6:33386800-33387600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:33386800-33387600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:33386800-33387600	Enhancers	Adipose Nuclei	Adipose
42	chr6:33386800-33387600	Enhancers	Brain Substantia Nigra	brain
43	chr6:33386800-33387600	Weak transcription	Colonic Mucosa	Colon
44	chr6:33386800-33387600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr6:33386800-33387600	Enhancers	Fetal Brain Male	brain
46	chr6:33386800-33387600	Enhancers	Fetal Kidney	kidney
47	chr6:33386800-33387600	Enhancers	Fetal Muscle Leg	muscle
48	chr6:33386800-33387600	Weak transcription	Psoas Muscle	Psoas
49	chr6:33386800-33387600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr6:33386800-33387600	Weak transcription	HSMM	muscle

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