Variant report

Variant	rs6806460
Chromosome Location	chr3:119816159-119816160
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	CEBPB	chr3:119816148-119816388	Hela-S3	cervix:	n/a	chr3:119816337-119816350 chr3:119816337-119816348 chr3:119816281-119816292 chr3:119816336-119816353
2	CEBPB	chr3:119816154-119816382	A549	lung:	n/a	chr3:119816337-119816350 chr3:119816337-119816348 chr3:119816281-119816292 chr3:119816336-119816353
3	POLR2A	chr3:119811576-119817111	MCF10A-Er-Src	breast:	n/a	n/a
4	TEAD4	chr3:119816029-119816469	HepG2	liver:	n/a	n/a
5	CEBPB	chr3:119816158-119816457	HepG2	liver:	n/a	chr3:119816337-119816350 chr3:119816337-119816348 chr3:119816281-119816292 chr3:119816336-119816353
6	POLR2A	chr3:119816114-119816379	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:119815520-119816302	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119812158..119817554-chr3:119829250..119832588,6	K562	blood:
2	chr3:119181413..119183027-chr3:119814257..119816285,2	MCF-7	breast:
3	chr3:119815352..119817379-chr3:119819963..119822983,3	K562	blood:
4	chr3:119814526..119816268-chr3:119818029..119819760,2	K562	blood:
5	chr3:119812621..119817617-chr3:119824950..119830930,7	K562	blood:
6	chr3:119655041..119657977-chr3:119815420..119818415,2	K562	blood:
7	chr3:119812799..119816595-chr3:119829619..119835566,15	MCF-7	breast:
8	chr3:119408612..119410162-chr3:119814493..119816849,2	K562	blood:
9	chr3:119814026..119816300-chr3:120067212..120070079,2	MCF-7	breast:
10	chr3:119647743..119650107-chr3:119815940..119817594,2	MCF-7	breast:
11	chr3:119776406..119778250-chr3:119816051..119818083,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1I2-1	chr3:119813266-119819259	NONHSAT091417

Variant related genes	Relation type
GSK3B	TF binding region
ENSG00000240661	Chromatin interaction
ENSG00000244308	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000163428	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs184576	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119808000-119816400	Active TSS	Fetal Brain Female	brain
2	chr3:119809000-119816200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:119809200-119816200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:119810000-119816200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:119810000-119816200	Active TSS	K562	blood
6	chr3:119810200-119816400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:119814600-119830600	Weak transcription	Gastric	stomach
8	chr3:119815000-119818000	Enhancers	Small Intestine	intestine
9	chr3:119815000-119829200	Weak transcription	Ovary	ovary
10	chr3:119815200-119816200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:119815200-119816400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr3:119815200-119816400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:119815200-119816400	Enhancers	Stomach Mucosa	stomach
14	chr3:119815200-119817000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr3:119815200-119817600	Enhancers	Placenta	Placenta
16	chr3:119815200-119819000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:119815200-119822000	Weak transcription	Esophagus	oesophagus
18	chr3:119815400-119816200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:119815400-119816200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:119815400-119816200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:119815400-119816200	Enhancers	Fetal Muscle Trunk	muscle
22	chr3:119815400-119816200	Enhancers	Fetal Muscle Leg	muscle
23	chr3:119815400-119816200	Enhancers	Fetal Thymus	thymus
24	chr3:119815400-119816200	Enhancers	Rectal Smooth Muscle	rectum
25	chr3:119815400-119816200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:119815400-119816400	Enhancers	Liver	Liver
27	chr3:119815400-119816400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:119815400-119816400	Enhancers	Fetal Brain Male	brain
29	chr3:119815400-119816600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:119815400-119816600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr3:119815400-119816600	Enhancers	Duodenum Mucosa	Duodenum
32	chr3:119815400-119816600	Enhancers	Fetal Heart	heart
33	chr3:119815400-119816600	Active TSS	HMEC	breast
34	chr3:119815400-119816600	Enhancers	HUVEC	blood vessel
35	chr3:119815400-119816600	Enhancers	Osteobl	bone
36	chr3:119815400-119817200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:119815400-119817200	Weak transcription	Fetal Intestine Small	intestine
38	chr3:119815400-119817600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:119815400-119817600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:119815400-119817800	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr3:119815400-119818400	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:119815400-119819600	Weak transcription	Primary T cells from cord blood	blood
43	chr3:119815400-119819600	Weak transcription	HSMMtube	muscle
44	chr3:119815400-119821000	Weak transcription	Adipose Nuclei	Adipose
45	chr3:119815400-119821000	Weak transcription	NH-A	brain
46	chr3:119815400-119821600	Weak transcription	Psoas Muscle	Psoas
47	chr3:119815400-119828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:119815400-119828200	Weak transcription	Aorta	Aorta
49	chr3:119815400-119828800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:119815400-119830000	Weak transcription	Fetal Lung	lung

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