Variant report

Variant	rs12093600
Chromosome Location	chr1:227059403-227059404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227058393..227060106-chr1:227070481..227073137,2	MCF-7	breast:
2	chr1:227058010..227060717-chr1:227127922..227130467,2	K562	blood:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10916055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10916058	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12057817	1.00[AMR][1000 genomes]
rs12085233	1.00[AMR][1000 genomes]
rs12094178	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1341281	1.00[AMR][1000 genomes]
rs1341282	1.00[AMR][1000 genomes]
rs6426539	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3381082	chr1:227029266-227059927	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227057800-227059600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:227057800-227059800	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr1:227057800-227060600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:227058600-227059600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr1:227058600-227059600	Flanking Active TSS	Colonic Mucosa	Colon
6	chr1:227058600-227059800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:227058600-227060000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:227058600-227060000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:227058800-227059600	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr1:227058800-227059600	Flanking Active TSS	Liver	Liver
11	chr1:227058800-227059600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr1:227058800-227059600	Flanking Active TSS	Stomach Mucosa	stomach
13	chr1:227058800-227059800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr1:227058800-227059800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:227058800-227059800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr1:227058800-227060000	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr1:227058800-227060000	Flanking Active TSS	Hela-S3	cervix
18	chr1:227058800-227060000	Flanking Active TSS	HSMM	muscle
19	chr1:227058800-227060200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr1:227059000-227059600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
21	chr1:227059000-227059600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:227059000-227059600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr1:227059000-227059600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
24	chr1:227059000-227059600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
25	chr1:227059000-227059600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:227059000-227059600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:227059000-227059600	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr1:227059000-227059600	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr1:227059000-227059600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr1:227059000-227059600	Bivalent Enhancer	Fetal Thymus	thymus
31	chr1:227059000-227059800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:227059000-227059800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:227059000-227059800	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr1:227059000-227059800	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr1:227059000-227059800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr1:227059000-227059800	Flanking Active TSS	NHLF	lung
37	chr1:227059000-227060000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr1:227059000-227060000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:227059000-227060000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr1:227059000-227060000	Bivalent Enhancer	Fetal Lung	lung
41	chr1:227059000-227060000	Flanking Active TSS	Fetal Muscle Trunk	muscle
42	chr1:227059000-227060000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
43	chr1:227059000-227060000	Enhancers	Small Intestine	intestine
44	chr1:227059000-227060000	Enhancers	Spleen	Spleen
45	chr1:227059000-227060400	Flanking Active TSS	HSMMtube	muscle
46	chr1:227059000-227061800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr1:227059000-227066800	Weak transcription	Aorta	Aorta
48	chr1:227059200-227059600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:227059200-227059600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:227059200-227059600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links