Variant report

Variant	rs71414546
Chromosome Location	chr2:55378219-55378220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55276124..55278386-chr2:55377199..55379824,2	MCF-7	breast:
2	chr2:55371026..55375430-chr2:55375600..55379751,6	K562	blood:
3	chr2:55366215..55370313-chr2:55376970..55382641,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf63-1	chr2:55378213-55378338	XLOC_002098

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1134722	0.84[EUR][1000 genomes]
rs11686766	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11686912	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11687876	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12989854	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12995548	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13000786	0.84[EUR][1000 genomes]
rs13003020	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13012567	0.84[EUR][1000 genomes]
rs13014752	0.84[EUR][1000 genomes]
rs13017468	0.84[EUR][1000 genomes]
rs2028139	0.86[EUR][1000 genomes]
rs34447956	0.84[EUR][1000 genomes]
rs35141050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183885	0.86[EUR][1000 genomes]
rs35227659	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35297827	0.83[EUR][1000 genomes]
rs35700883	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36121000	0.84[EUR][1000 genomes]
rs4318424	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4627623	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742306	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6743339	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6747466	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71414544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71414549	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71414556	0.84[EUR][1000 genomes]
rs71414557	0.84[EUR][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	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55361800-55378600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:55365200-55381000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:55365600-55378600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:55366200-55378600	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:55367200-55378800	Weak transcription	Placenta	Placenta
6	chr2:55369800-55378600	Weak transcription	Fetal Stomach	stomach
7	chr2:55370000-55379600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:55371600-55382400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:55373400-55381000	Weak transcription	Stomach Mucosa	stomach
10	chr2:55373800-55378600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:55375200-55378400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr2:55375800-55379600	Weak transcription	K562	blood
13	chr2:55376000-55378400	Weak transcription	HSMMtube	muscle
14	chr2:55376000-55378400	Weak transcription	NHLF	lung
15	chr2:55376000-55378800	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:55376000-55378800	Weak transcription	Osteobl	bone
17	chr2:55376000-55379400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:55376000-55380400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:55376000-55381000	Weak transcription	Fetal Thymus	thymus
20	chr2:55376000-55381000	Weak transcription	HSMM	muscle
21	chr2:55376000-55383800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:55376200-55378800	Weak transcription	NHDF-Ad	bronchial
23	chr2:55376200-55379000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:55376200-55379200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:55376200-55379400	Weak transcription	NHEK	skin
26	chr2:55376400-55380800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:55376600-55378600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:55376800-55378800	Weak transcription	Lung	lung
29	chr2:55376800-55382000	Enhancers	Primary B cells from peripheral blood	blood
30	chr2:55376800-55382400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr2:55377400-55380200	Weak transcription	Hela-S3	cervix
32	chr2:55377400-55381800	Enhancers	GM12878-XiMat	blood
33	chr2:55377400-55382000	Enhancers	Primary B cells from cord blood	blood
34	chr2:55377600-55381000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:55377600-55381800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr2:55378000-55386800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:55378000-55386800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:55378200-55379400	Enhancers	Brain Anterior Caudate	brain
39	chr2:55378200-55380200	Enhancers	Brain Angular Gyrus	brain
40	chr2:55378200-55381000	Enhancers	Stomach Smooth Muscle	stomach
41	chr2:55378200-55382400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:55378200-55383600	Enhancers	Brain Substantia Nigra	brain
43	chr2:55378200-55386200	Enhancers	Brain Hippocampus Middle	brain
44	chr2:55378200-55388000	Enhancers	Brain Cingulate Gyrus	brain
45	chr2:55378200-55388800	Enhancers	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links