Variant report

Variant	rs2417580
Chromosome Location	chr12:10378690-10378691
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10363710..10369534-chr12:10376619..10381190,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GABARAPL1-3	chr12:10378665-10378832	NONHSAT026875

Variant related genes	Relation type
ENSG00000139112	Chromatin interaction
ENSG00000255958	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10734821	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10743874	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10743875	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10845099	0.85[AMR][1000 genomes]
rs11053709	0.90[EUR][1000 genomes]
rs11830137	0.82[EUR][1000 genomes]
rs4254156	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4325390	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4764331	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs765790	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7966224	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1054811	chr12:10350587-10440005	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10366800-10386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:10368400-10380200	Weak transcription	GM12878-XiMat	blood
3	chr12:10368400-10380400	Weak transcription	Dnd41	blood
4	chr12:10372800-10379600	Weak transcription	Right Atrium	heart
5	chr12:10373400-10382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:10374400-10378800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:10375200-10379000	Weak transcription	Hela-S3	cervix
8	chr12:10375200-10379600	Weak transcription	Thymus	Thymus
9	chr12:10375200-10380000	Weak transcription	Small Intestine	intestine
10	chr12:10375400-10379600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:10375400-10380600	Weak transcription	Fetal Lung	lung
12	chr12:10375600-10380400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:10376000-10379600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:10376400-10380200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:10376400-10380200	Weak transcription	Gastric	stomach
16	chr12:10376400-10380400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:10376400-10380400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:10376400-10386600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:10376400-10386600	Weak transcription	Brain Substantia Nigra	brain
20	chr12:10376400-10388600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr12:10376400-10395000	Weak transcription	Pancreas	Pancrea
22	chr12:10376400-10397600	Weak transcription	Aorta	Aorta
23	chr12:10376600-10378800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:10376600-10378800	Weak transcription	Brain Germinal Matrix	brain
25	chr12:10376600-10379200	Weak transcription	HUVEC	blood vessel
26	chr12:10376600-10380000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr12:10376600-10380400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:10376600-10382400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr12:10376600-10385600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:10376800-10379000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:10376800-10379200	Weak transcription	Fetal Brain Male	brain
32	chr12:10376800-10380000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:10376800-10380400	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:10376800-10385800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:10377000-10378800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:10377000-10378800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:10377000-10378800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:10377000-10378800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:10377000-10378800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:10377000-10378800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:10377000-10379400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:10377000-10380000	Weak transcription	Primary T cells from cord blood	blood
43	chr12:10377000-10380200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:10377000-10382800	Weak transcription	Right Ventricle	heart
45	chr12:10377000-10385000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:10377000-10386600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:10377200-10378800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:10377200-10379000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:10377200-10379000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:10377200-10379000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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