Variant report

Variant	rs55677077
Chromosome Location	chr12:50219508-50219509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50219161-50219590	U87	brain:	n/a	n/a
2	NANOG	chr12:50219199-50219564	H1-hESC	embryonic stem cell:	n/a	n/a
3	RFX5	chr12:50218552-50220875	IMR90	lung:	n/a	chr12:50219337-50219352 chr12:50219050-50219059
4	SIN3A	chr12:50219093-50219568	H1-hESC	embryonic stem cell:	n/a	n/a
5	RFX5	chr12:50219141-50219559	H1-hESC	embryonic stem cell:	n/a	chr12:50219337-50219352
6	POLR2A	chr12:50219185-50219590	U87	brain:	n/a	n/a
7	SPI1	chr12:50218605-50219529	HL-60	blood:	n/a	chr12:50219150-50219163 chr12:50219267-50219280
8	RFX5	chr12:50219178-50219546	GM12878	blood:	n/a	chr12:50219337-50219352
9	ZNF143	chr12:50219410-50219628	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50216203..50220741-chr12:50220862..50224448,8	MCF-7	breast:
2	chr12:50209248..50211302-chr12:50219321..50221793,2	K562	blood:
3	chr12:50200144..50201863-chr12:50219253..50221982,2	MCF-7	breast:
4	chr12:50216965..50224421-chr12:50234869..50238255,17	MCF-7	breast:
5	chr12:50203774..50205961-chr12:50217957..50219971,2	K562	blood:
6	chr12:50197055..50201000-chr12:50217056..50221303,4	K562	blood:
7	chr12:50137650..50140394-chr12:50217891..50219857,2	MCF-7	breast:
8	chr12:50198169..50199733-chr12:50218662..50220771,2	K562	blood:
9	chr12:50134227..50139526-chr12:50218668..50224471,9	K562	blood:
10	chr12:50181461..50183796-chr12:50216518..50220004,3	MCF-7	breast:
11	chr12:50133925..50140140-chr12:50217980..50223924,8	K562	blood:
12	chr12:50217971..50224800-chr12:50231213..50239207,27	MCF-7	breast:

No data

Variant related genes	Relation type
BCDIN3D-AS1	TF binding region
ENSG00000139644	Chromatin interaction
ENSG00000167566	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000258057	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1031477	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875976	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169166	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169170	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4898534	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4898535	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55758326	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66908137	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7953539	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973894	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50197600-50220400	Weak transcription	A549	lung
2	chr12:50203600-50219800	Weak transcription	Aorta	Aorta
3	chr12:50204400-50220200	Weak transcription	Fetal Kidney	kidney
4	chr12:50205200-50220000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:50208800-50221200	Weak transcription	Small Intestine	intestine
6	chr12:50214400-50220200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr12:50214400-50220800	Enhancers	Placenta	Placenta
8	chr12:50215200-50221000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:50215400-50219600	Weak transcription	Liver	Liver
10	chr12:50215800-50219600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:50215800-50220600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:50215800-50221200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:50216000-50220000	Weak transcription	Thymus	Thymus
14	chr12:50216000-50221000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:50216000-50221000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:50216200-50220000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:50216200-50220600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr12:50216200-50220800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:50216400-50219800	Weak transcription	Primary T cells from cord blood	blood
20	chr12:50216600-50220200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:50216800-50220600	Weak transcription	Psoas Muscle	Psoas
22	chr12:50217000-50220200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:50217200-50220000	Enhancers	Colon Smooth Muscle	Colon
24	chr12:50217200-50220400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:50217200-50221000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:50217400-50220600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:50217400-50220600	Enhancers	Duodenum Mucosa	Duodenum
28	chr12:50217600-50220400	Enhancers	Fetal Heart	heart
29	chr12:50217600-50220600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:50217600-50220800	Enhancers	Brain Anterior Caudate	brain
31	chr12:50217800-50219600	Strong transcription	Fetal Intestine Small	intestine
32	chr12:50217800-50220200	Enhancers	Fetal Brain Male	brain
33	chr12:50217800-50220400	Enhancers	Brain Cingulate Gyrus	brain
34	chr12:50217800-50220600	Enhancers	Brain Substantia Nigra	brain
35	chr12:50217800-50220800	Enhancers	Fetal Thymus	thymus
36	chr12:50217800-50221200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:50217800-50221600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr12:50218000-50219600	Genic enhancers	Fetal Stomach	stomach
39	chr12:50218000-50220600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:50218000-50220600	Enhancers	HUVEC	blood vessel
41	chr12:50218000-50220800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:50218000-50220800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr12:50218200-50219600	Flanking Active TSS	Osteobl	bone
44	chr12:50218200-50220000	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr12:50218200-50220200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:50218200-50220400	Enhancers	Primary B cells from cord blood	blood
47	chr12:50218200-50220400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
48	chr12:50218200-50220600	Enhancers	H1 Cell Line	embryonic stem cell
49	chr12:50218200-50220600	Weak transcription	Fetal Intestine Large	intestine
50	chr12:50218200-50221000	Enhancers	Primary hematopoietic stem cells	blood

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