Variant report

Variant	rs12621292
Chromosome Location	chr2:54949615-54949616
allele	C/T
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	RFX5	chr2:54949181-54951799	IMR90	lung:	n/a	chr2:54950701-54950716
2	POLR2A	chr2:54949527-54950069	U87	brain:	n/a	n/a
3	POLR2A	chr2:54949535-54950069	U87	brain:	n/a	n/a
4	MXI1	chr2:54949356-54954156	SK-N-SH	brain:	n/a	chr2:54949674-54949689
5	POLR2A	chr2:54949471-54951074	U87	brain:	n/a	n/a
6	HCFC1	chr2:54949547-54951672	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr2:54949584-54951068	U87	brain:	n/a	n/a
8	SREBP1	chr2:54949596-54951061	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:54949557-54950675	MCF10A-Er-Src	breast:	n/a	n/a
10	MXI1	chr2:54949594-54952119	IMR90	lung:	n/a	chr2:54949674-54949689

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54942542..54944647-chr2:54947416..54949799,3	K562	blood:
2	chr2:54785416..54786973-chr2:54949128..54950959,2	K562	blood:

Variant related genes	Relation type
EML6	TF binding region
ENSG00000115306	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12615160	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12615229	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12621943	0.86[ASN][1000 genomes]
rs241660	0.85[ASN][1000 genomes]
rs354220	0.85[ASN][1000 genomes]
rs3769332	0.84[JPT][hapmap];1.00[EUR][1000 genomes]
rs3769333	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54945200-54950000	Weak transcription	Right Atrium	heart
2	chr2:54948000-54949800	Weak transcription	Pancreas	Pancrea
3	chr2:54949400-54949800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:54949400-54949800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:54949400-54949800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:54949400-54949800	Enhancers	NHDF-Ad	bronchial
7	chr2:54949400-54950400	Flanking Active TSS	K562	blood
8	chr2:54949600-54949800	Enhancers	H1 Cell Line	embryonic stem cell
9	chr2:54949600-54949800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:54949600-54949800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
11	chr2:54949600-54949800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr2:54949600-54949800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
13	chr2:54949600-54949800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:54949600-54949800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:54949600-54949800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:54949600-54949800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr2:54949600-54949800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:54949600-54949800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:54949600-54949800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:54949600-54949800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:54949600-54949800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:54949600-54949800	Enhancers	Brain Anterior Caudate	brain
23	chr2:54949600-54949800	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:54949600-54949800	Enhancers	Brain Hippocampus Middle	brain
25	chr2:54949600-54949800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr2:54949600-54949800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:54949600-54949800	Enhancers	Brain Substantia Nigra	brain
28	chr2:54949600-54949800	Active TSS	Colonic Mucosa	Colon
29	chr2:54949600-54949800	Enhancers	Colon Smooth Muscle	Colon
30	chr2:54949600-54949800	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr2:54949600-54949800	Enhancers	Fetal Intestine Large	intestine
32	chr2:54949600-54949800	Enhancers	Fetal Intestine Small	intestine
33	chr2:54949600-54949800	Enhancers	Fetal Kidney	kidney
34	chr2:54949600-54949800	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr2:54949600-54949800	Enhancers	Fetal Thymus	thymus
36	chr2:54949600-54949800	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr2:54949600-54949800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr2:54949600-54949800	Enhancers	Rectal Smooth Muscle	rectum
39	chr2:54949600-54949800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:54949600-54949800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr2:54949600-54949800	Enhancers	Stomach Smooth Muscle	stomach
42	chr2:54949600-54949800	Active TSS	Thymus	Thymus
43	chr2:54949600-54949800	Enhancers	HMEC	breast
44	chr2:54949600-54949800	Enhancers	HSMM	muscle
45	chr2:54949600-54949800	Enhancers	HSMMtube	muscle
46	chr2:54949600-54949800	Enhancers	HUVEC	blood vessel
47	chr2:54949600-54949800	Enhancers	NH-A	brain
48	chr2:54949600-54949800	Enhancers	NHLF	lung
49	chr2:54949600-54950000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
50	chr2:54949600-54950000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links