Variant report

Variant	rs2463173
Chromosome Location	chr12:118593032-118593033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118587254..118590333-chr12:118591083..118593849,3	K562	blood:
2	chr12:118591162..118593409-chr12:118596850..118598806,2	K562	blood:
3	chr12:118592379..118594446-chr12:118829106..118831111,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135090	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1051175	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1092854	0.81[ASN][1000 genomes]
rs1277175	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1726386	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1726407	0.91[EUR][1000 genomes]
rs2018619	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2249624	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353886	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs353887	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs353889	0.84[ASN][1000 genomes]
rs353896	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs364823	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs795473	0.87[ASN][1000 genomes]
rs795481	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs795482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1054703	chr12:118575000-118638613	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv541611	chr12:118575000-118638613	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118575600-118601600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:118576000-118601200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:118576000-118619600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:118576000-118624000	Weak transcription	Stomach Mucosa	stomach
5	chr12:118576200-118595400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:118577400-118601800	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:118577600-118599000	Weak transcription	Psoas Muscle	Psoas
8	chr12:118578200-118611600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:118578600-118603200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:118583800-118595400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:118583800-118598000	Weak transcription	HUVEC	blood vessel
12	chr12:118584000-118595000	Weak transcription	HSMMtube	muscle
13	chr12:118584000-118595200	Weak transcription	HSMM	muscle
14	chr12:118584000-118595600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:118584000-118627600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:118584200-118595200	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:118585600-118603000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:118585800-118597400	Weak transcription	Hela-S3	cervix
19	chr12:118585800-118619000	Weak transcription	HepG2	liver
20	chr12:118586200-118601000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:118586200-118619400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:118586400-118595200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:118586600-118595400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:118586600-118595600	Weak transcription	Fetal Heart	heart
25	chr12:118586600-118613600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:118586800-118600400	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:118586800-118600800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:118586800-118601400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:118586800-118603600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:118587000-118600400	Strong transcription	Primary T cells from cord blood	blood
31	chr12:118587600-118611200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:118587600-118619200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:118587800-118620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:118588000-118595200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:118589000-118601200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:118589200-118597400	Weak transcription	Small Intestine	intestine
37	chr12:118589200-118597600	Weak transcription	NH-A	brain
38	chr12:118589400-118601200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:118589600-118619000	Weak transcription	A549	lung
40	chr12:118590000-118595400	Weak transcription	HMEC	breast
41	chr12:118590200-118594000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:118590200-118595000	Weak transcription	Placenta	Placenta
43	chr12:118590200-118595200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:118590200-118595400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr12:118590200-118595400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:118590400-118593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:118590400-118593600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:118590400-118593800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:118590400-118593800	Weak transcription	Left Ventricle	heart
50	chr12:118590400-118594600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links