Variant report

Variant	rs549025257
Chromosome Location	chr1:186647804-186647805
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	chr1:186647362-186650832	PBDE	blood:	n/a	n/a
2	POLR2A	chr1:186647276-186650764	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:186646993-186651195	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:186647690-186648098	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:186647207-186651362	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186641962..186644518-chr1:186645424..186648177,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273129	TF binding region
PTGS2	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv470750	chr1:186642429-186700959	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv548403	chr1:186642429-186700959	Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv872595	chr1:186646005-186649485	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
8	nsv872596	chr1:186646480-186649308	Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv872597	chr1:186646480-186649485	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
10	nsv548404	chr1:186647104-186649308	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186632800-186649000	Weak transcription	Fetal Lung	lung
2	chr1:186639400-186648400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:186640800-186648000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:186640800-186648200	Weak transcription	Brain Angular Gyrus	brain
5	chr1:186640800-186649200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:186641600-186648400	Weak transcription	NHLF	lung
7	chr1:186641800-186648400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:186642200-186649200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:186642200-186649200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:186642400-186649200	Weak transcription	Gastric	stomach
11	chr1:186642600-186648200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:186644000-186648400	Weak transcription	Adipose Nuclei	Adipose
13	chr1:186644200-186649000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:186644200-186649000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:186644200-186649000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:186644200-186649200	Weak transcription	Lung	lung
17	chr1:186644400-186648400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:186644400-186649000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:186644400-186649200	Weak transcription	Aorta	Aorta
20	chr1:186644600-186648200	Weak transcription	Fetal Stomach	stomach
21	chr1:186644600-186648800	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:186644600-186649000	Weak transcription	Ovary	ovary
23	chr1:186645200-186648000	Strong transcription	Osteobl	bone
24	chr1:186645800-186648400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:186645800-186649200	Weak transcription	Spleen	Spleen
26	chr1:186646000-186648200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:186646000-186648200	Weak transcription	NH-A	brain
28	chr1:186646400-186648400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:186646400-186651000	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr1:186646600-186648000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:186646600-186648200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
32	chr1:186646800-186649200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:186647000-186648200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:186647000-186652000	Active TSS	Stomach Smooth Muscle	stomach
35	chr1:186647600-186648200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:186647600-186648400	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
37	chr1:186647600-186648600	Flanking Active TSS	HUVEC	blood vessel
38	chr1:186647600-186651000	Active TSS	A549	lung
39	chr1:186647800-186648000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:186647800-186648000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:186647800-186648000	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr1:186647800-186648000	Transcr. at gene 5' and 3'	HMEC	breast
43	chr1:186647800-186648000	Flanking Active TSS	NHDF-Ad	bronchial
44	chr1:186647800-186648200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:186647800-186648200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:186647800-186648200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
47	chr1:186647800-186648400	Genic enhancers	Primary monocytes fromperipheralblood	blood
48	chr1:186647800-186648400	Active TSS	Primary B cells from cord blood	blood
49	chr1:186647800-186648600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:186647800-186648600	Flanking Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links