Variant report

Variant	rs12824458
Chromosome Location	chr12:49627819-49627820
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:34)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49624204..49632381-chr12:49656851..49664182,36	K562	blood:
2	chr12:49484424..49486787-chr12:49626950..49628768,2	K562	blood:
3	chr12:49495156..49497539-chr12:49627737..49630589,2	MCF-7	breast:
4	chr12:49504257..49506648-chr12:49625633..49628380,2	MCF-7	breast:
5	chr12:49451583..49453085-chr12:49626794..49628619,2	K562	blood:
6	chr12:49627091..49630045-chr12:49647467..49650114,2	MCF-7	breast:
7	chr12:49581061..49584023-chr12:49626756..49629853,3	K562	blood:
8	chr12:49619700..49621201-chr12:49627678..49629883,2	MCF-7	breast:
9	chr12:49524620..49525974-chr12:49627554..49629013,4	NB4	blood:
10	chr12:49454829..49457551-chr12:49626042..49628267,3	K562	blood:
11	chr12:49410482..49414207-chr12:49626901..49628539,3	K562	blood:
12	chr12:49480667..49484099-chr12:49627128..49630502,6	K562	blood:
13	chr12:49452614..49454343-chr12:49626928..49628494,2	MCF-7	breast:
14	chr12:49523058..49526558-chr12:49627579..49630702,9	MCF-7	breast:
15	chr12:49617947..49619571-chr12:49625520..49628045,3	K562	blood:
16	chr12:49626870..49630016-chr12:49656039..49660011,4	MCF-7	breast:
17	chr12:49582252..49584303-chr12:49626991..49629513,3	MCF-7	breast:
18	chr12:49626903..49627870-chr3:25824407..25824933,2	NB4	blood:
19	chr12:49624371..49632888-chr12:49655742..49664182,29	K562	blood:
20	chr12:49502278..49504083-chr12:49627127..49629161,2	K562	blood:
21	chr12:49518847..49527600-chr12:49624546..49632235,69	K562	blood:
22	chr12:49626415..49629874-chr12:49642724..49645857,3	MCF-7	breast:
23	chr12:49626201..49630727-chr12:49631926..49634972,10	K562	blood:
24	chr12:49627452..49628272-chr17:41465817..41466453,2	NB4	blood:
25	chr12:49611550..49615135-chr12:49626761..49630349,3	MCF-7	breast:
26	chr12:49625768..49629972-chr12:49657225..49660229,8	MCF-7	breast:
27	chr12:49451583..49453949-chr12:49625558..49628294,2	K562	blood:
28	chr12:49484658..49486546-chr12:49627171..49629084,2	K562	blood:
29	chr12:49487030..49490024-chr12:49627022..49629311,2	K562	blood:
30	chr12:49523889..49527940-chr12:49626125..49630578,10	MCF-7	breast:
31	chr12:49580612..49583821-chr12:49626954..49630010,6	MCF-7	breast:
32	chr12:49513866..49528454-chr12:49616957..49635747,92	K562	blood:
33	chr12:49579518..49583719-chr12:49624804..49628256,4	K562	blood:
34	chr12:49498025..49500103-chr12:49626582..49628144,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TUBA1A-1	chr12:49627352-49627921	ENSG00000258101.1

No data

Variant related genes	Relation type
ENSG00000139636	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000167552	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000151092	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000151093	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000200309	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10467103	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11168921	0.84[AMR][1000 genomes]
rs11168930	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34367716	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59976042	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68128447	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv518041	chr12:49618043-49645240	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49624000-49628400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr12:49625600-49628000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr12:49625600-49628200	Flanking Active TSS	HSMMtube	muscle
4	chr12:49625600-49628400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:49625600-49628400	Enhancers	Placenta	Placenta
6	chr12:49625800-49628400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:49625800-49628400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr12:49625800-49628400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr12:49625800-49628400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:49625800-49628400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:49625800-49628400	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr12:49625800-49629400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:49626000-49628000	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr12:49626000-49628200	Flanking Active TSS	Colon Smooth Muscle	Colon
15	chr12:49626200-49628400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
16	chr12:49626200-49628400	Enhancers	Fetal Intestine Small	intestine
17	chr12:49626200-49629000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr12:49626400-49628400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr12:49626400-49628400	Flanking Active TSS	NH-A	brain
20	chr12:49626600-49628200	Flanking Active TSS	Fetal Brain Male	brain
21	chr12:49626600-49628200	Enhancers	Ovary	ovary
22	chr12:49626600-49628200	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr12:49626600-49628400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr12:49626600-49628400	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr12:49626600-49629400	Enhancers	Spleen	Spleen
26	chr12:49626800-49628200	Enhancers	Pancreas	Pancrea
27	chr12:49626800-49628400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:49626800-49628400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:49626800-49628400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:49626800-49628400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr12:49626800-49628400	Enhancers	Left Ventricle	heart
32	chr12:49626800-49629000	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr12:49626800-49629200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr12:49626800-49629200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:49626800-49629200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:49627000-49628000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:49627000-49628200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:49627000-49628200	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr12:49627000-49628200	Flanking Active TSS	Fetal Brain Female	brain
40	chr12:49627000-49628200	Enhancers	Psoas Muscle	Psoas
41	chr12:49627000-49628200	Enhancers	Right Ventricle	heart
42	chr12:49627000-49628400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:49627000-49628400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:49627000-49628400	Flanking Active TSS	K562	blood
45	chr12:49627200-49628000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
46	chr12:49627200-49628000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr12:49627200-49628000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr12:49627200-49628200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr12:49627200-49628200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:49627200-49628200	Flanking Active TSS	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links