Variant report

Variant	rs10876854
Chromosome Location	chr12:56220839-56220840
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56220800-56220842	K562	blood:	n/a	n/a
2	POLR2A	chr12:56220836-56225418	SK-N-MC	brain:	n/a	n/a
3	PAX5	chr12:56220293-56220856	GM12878	blood:	n/a	n/a
4	ZNF384	chr12:56220435-56221227	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56119665..56125098-chr12:56220794..56225708,11	MCF-7	breast:
2	chr12:56217816..56225905-chr12:56319649..56327312,13	K562	blood:
3	chr12:56217992..56226798-chr12:56311494..56331042,68	MCF-7	breast:
4	chr12:56219783..56227072-chr12:56318292..56323886,14	K562	blood:
5	chr12:56217492..56232243-chr12:56318854..56330686,48	MCF-7	breast:
6	chr12:56220285..56224153-chr12:56233677..56238372,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257390	TF binding region
TMEM198B	TF binding region
ENSG00000258056	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000123342	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1081732	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10876851	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10876852	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12372076	0.93[ASN][1000 genomes]
rs1681087	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2694012	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7305787	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs772262	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs772263	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7954619	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7954839	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7965333	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56213000-56221000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:56213400-56221000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:56216400-56221000	Weak transcription	Small Intestine	intestine
4	chr12:56216600-56221000	Weak transcription	Aorta	Aorta
5	chr12:56216800-56221000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:56217000-56221000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:56217000-56221000	Enhancers	HepG2	liver
8	chr12:56217000-56221200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:56217200-56221000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:56217200-56221000	Weak transcription	Lung	lung
11	chr12:56217200-56221000	Weak transcription	Ovary	ovary
12	chr12:56217200-56221000	Weak transcription	Right Ventricle	heart
13	chr12:56217200-56221000	Weak transcription	NHLF	lung
14	chr12:56217200-56221200	Weak transcription	Esophagus	oesophagus
15	chr12:56217400-56221000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:56217400-56221000	Weak transcription	Psoas Muscle	Psoas
17	chr12:56217400-56221000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:56217400-56221000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:56217400-56221000	Weak transcription	NH-A	brain
20	chr12:56217400-56222400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:56217400-56222400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:56217400-56222600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:56217600-56221000	Weak transcription	HSMMtube	muscle
24	chr12:56217800-56221000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:56217800-56221200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:56217800-56221200	Enhancers	Liver	Liver
27	chr12:56218000-56221000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:56218000-56221000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:56218000-56221600	Weak transcription	Fetal Kidney	kidney
30	chr12:56218000-56222200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:56218000-56222600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:56218200-56221000	Enhancers	Brain Angular Gyrus	brain
33	chr12:56218200-56221000	Enhancers	Brain Hippocampus Middle	brain
34	chr12:56218200-56221000	Enhancers	Fetal Brain Male	brain
35	chr12:56218200-56221200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr12:56218200-56222200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:56218200-56222400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:56218200-56222600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:56218200-56222600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:56218400-56221000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr12:56218400-56221000	Weak transcription	NHDF-Ad	bronchial
42	chr12:56218400-56221200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr12:56218400-56222400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr12:56218400-56222600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:56218600-56221000	Weak transcription	A549	lung
46	chr12:56218600-56221200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr12:56218600-56222400	Enhancers	Adipose Nuclei	Adipose
48	chr12:56218600-56222600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr12:56218800-56221000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:56218800-56221400	Enhancers	Primary T cells from cord blood	blood

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