Variant report

Variant	rs775242
Chromosome Location	chr12:57999546-57999547
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr12:57998203-57999608	H1-hESC	embryonic stem cell:	n/a	chr12:57998248-57998257 chr12:57999287-57999295

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57998188..58000440-chr12:58014339..58016922,2	MCF-7	breast:
2	chr12:57999383..58001566-chr12:58144554..58147066,2	K562	blood:
3	chr12:57999349..58001291-chr12:58136626..58138684,2	MCF-7	breast:
4	chr12:57997608..58000545-chr12:58238111..58240464,2	MCF-7	breast:
5	chr12:57983454..57989400-chr12:57989791..58002327,29	MCF-7	breast:
6	chr12:57940405..57942301-chr12:57997757..58000737,2	MCF-7	breast:
7	chr12:57997114..58001112-chr12:58025485..58030490,5	MCF-7	breast:
8	chr12:57997150..58000080-chr12:58158932..58161067,2	MCF-7	breast:

No data

Variant related genes	Relation type
ARHGEF25	TF binding region
DTX3	TF binding region
ENSG00000135452	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000135454	Chromatin interaction
ENSG00000135502	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1284185	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1296041	0.86[EUR][1000 genomes]
rs1630692	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1678508	0.82[EUR][1000 genomes]
rs2599999	1.00[CEU][hapmap]
rs2620683	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs774894	1.00[CEU][hapmap]
rs810205	1.00[CEU][hapmap]
rs813516	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
6	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
7	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57993000-57999600	Weak transcription	K562	blood
2	chr12:57997600-57999600	Active TSS	Colon Smooth Muscle	Colon
3	chr12:57997800-57999600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:57997800-57999600	Active TSS	Aorta	Aorta
5	chr12:57997800-57999800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr12:57998000-57999600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:57998000-57999600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr12:57998000-57999600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr12:57998000-57999800	Flanking Active TSS	Thymus	Thymus
10	chr12:57998200-57999600	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr12:57998200-57999600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
12	chr12:57998200-57999600	Active TSS	Fetal Kidney	kidney
13	chr12:57998400-57999600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:57998400-57999800	Bivalent/Poised TSS	Psoas Muscle	Psoas
15	chr12:57998800-57999600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:57998800-57999600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:57998800-57999600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:57998800-57999600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
19	chr12:57998800-57999600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
20	chr12:57998800-57999600	Flanking Active TSS	Right Ventricle	heart
21	chr12:57999000-57999600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:57999000-57999600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:57999000-57999600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:57999000-57999600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:57999000-57999600	Flanking Active TSS	Fetal Heart	heart
26	chr12:57999000-57999600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
27	chr12:57999000-57999600	Flanking Active TSS	GM12878-XiMat	blood
28	chr12:57999000-57999600	Flanking Bivalent TSS/Enh	HepG2	liver
29	chr12:57999000-57999800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:57999000-57999800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:57999000-57999800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:57999000-57999800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:57999000-57999800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
34	chr12:57999000-57999800	Flanking Active TSS	Left Ventricle	heart
35	chr12:57999000-57999800	Flanking Active TSS	HSMMtube	muscle
36	chr12:57999000-58000000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr12:57999000-58000000	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr12:57999000-58000200	Flanking Active TSS	Fetal Brain Female	brain
39	chr12:57999200-57999600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:57999200-57999600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
41	chr12:57999200-57999600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:57999200-57999600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:57999200-57999600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:57999200-57999600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:57999200-57999600	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr12:57999200-57999600	Enhancers	Esophagus	oesophagus
47	chr12:57999200-57999600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr12:57999200-57999600	Flanking Active TSS	Right Atrium	heart
49	chr12:57999200-57999600	Bivalent/Poised TSS	Stomach Mucosa	stomach
50	chr12:57999200-57999600	Flanking Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links