Variant report

Variant	rs2842320
Chromosome Location	chr14:68944073-68944074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68942896..68944476-chr14:69282297..69284211,2	MCF-7	breast:
2	chr14:68941663..68944828-chr14:69250861..69253636,3	MCF-7	breast:
3	chr14:68938156..68939886-chr14:68942575..68944158,2	K562	blood:
4	chr14:68943541..68946317-chr14:68952367..68953897,2	MCF-7	breast:
5	chr14:68930492..68947840-chr14:69251918..69264148,62	MCF-7	breast:
6	chr14:68943293..68946100-chr14:69042850..69045174,2	MCF-7	breast:
7	chr14:68943428..68945388-chr14:69016683..69019444,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction
ENSG00000182185	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10454686	0.85[CEU][hapmap]
rs11158737	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11158742	1.00[JPT][hapmap]
rs12435006	1.00[JPT][hapmap]
rs12588330	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12889206	0.86[MEX][hapmap]
rs12897307	1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17755674	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1956538	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs2064910	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs2331703	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2331704	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2525507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2753403	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3784118	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs3966077	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs4899241	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4899243	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902571	0.90[CEU][hapmap];0.86[MEX][hapmap]
rs4902578	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs4902580	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4902581	1.00[JPT][hapmap]
rs4902582	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4902587	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4902588	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4902589	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6573834	0.86[MEX][hapmap]
rs66597987	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7140827	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7145422	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs7150454	0.86[MEX][hapmap]
rs72727487	0.92[ASN][1000 genomes]
rs8003606	1.00[CHB][hapmap]
rs8009876	0.86[MEX][hapmap]
rs8010430	0.92[ASN][1000 genomes]
rs8013026	0.85[CEU][hapmap]
rs8015516	0.90[CEU][hapmap]
rs8019592	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9323510	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9743896	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs975422	0.89[CEU][hapmap];1.00[JPT][hapmap]

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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2842320	C14orf50	cis	cerebellum	SCAN
rs2842320	NCRNA00238	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68928600-68949000	Weak transcription	Thymus	Thymus
2	chr14:68932200-68950000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr14:68933000-68946600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr14:68933600-68950600	Weak transcription	Aorta	Aorta
5	chr14:68934200-68946200	Enhancers	Primary B cells from peripheral blood	blood
6	chr14:68936000-68947600	Weak transcription	Primary T cells from cord blood	blood
7	chr14:68936800-68944800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr14:68938800-68944200	Enhancers	Liver	Liver
9	chr14:68939000-68947400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr14:68939000-68951600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr14:68940200-68949400	Weak transcription	Fetal Lung	lung
12	chr14:68941000-68944600	Enhancers	Fetal Intestine Large	intestine
13	chr14:68941200-68944400	Enhancers	NHEK	skin
14	chr14:68941200-68946400	Enhancers	HMEC	breast
15	chr14:68941600-68944200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr14:68941600-68945600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr14:68941800-68944600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr14:68942000-68944800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr14:68942000-68945400	Enhancers	Primary B cells from cord blood	blood
20	chr14:68942200-68944800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr14:68942400-68944200	Enhancers	HUVEC	blood vessel
22	chr14:68942400-68945200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:68942400-68945200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr14:68942400-68945800	Weak transcription	Fetal Intestine Small	intestine
25	chr14:68942600-68944200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:68942600-68944400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr14:68942600-68944400	Enhancers	NH-A	brain
28	chr14:68942600-68944800	Enhancers	Adipose Nuclei	Adipose
29	chr14:68942600-68945400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr14:68942600-68945600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr14:68942600-68946000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr14:68942600-68946600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr14:68942800-68944200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr14:68942800-68944200	Enhancers	Stomach Mucosa	stomach
35	chr14:68942800-68944200	Enhancers	Osteobl	bone
36	chr14:68942800-68944400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr14:68942800-68944400	Enhancers	HSMM	muscle
38	chr14:68942800-68944400	Enhancers	HSMMtube	muscle
39	chr14:68942800-68944400	Enhancers	NHLF	lung
40	chr14:68942800-68945400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr14:68943000-68944200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr14:68943000-68944200	Enhancers	Fetal Muscle Leg	muscle
43	chr14:68943000-68944200	Enhancers	Right Atrium	heart
44	chr14:68943000-68945000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr14:68943000-68947200	Enhancers	Placenta Amnion	Placenta Amnion
46	chr14:68943200-68944200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr14:68943200-68944800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr14:68943200-68944800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr14:68943200-68945200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr14:68943200-68946800	Enhancers	Pancreas	Pancrea

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