Variant report

Variant	rs4899243
Chromosome Location	chr14:68953817-68953818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:68951909..68954221-chr14:69252070..69254907,3	MCF-7	breast:
2	chr14:68934923..68936704-chr14:68952698..68955453,2	MCF-7	breast:
3	chr14:68946983..68949928-chr14:68952224..68954178,2	K562	blood:
4	chr14:68946730..68948878-chr14:68952615..68954751,2	K562	blood:
5	chr14:68943541..68946317-chr14:68952367..68953897,2	MCF-7	breast:
6	chr14:68928799..68930432-chr14:68953133..68955101,2	MCF-7	breast:
7	chr14:68947089..68949808-chr14:68953310..68954848,2	MCF-7	breast:
8	chr14:68953391..68956250-chr14:68958714..68961472,3	MCF-7	breast:
9	chr14:68953516..68956105-chr14:69031281..69032834,2	MCF-7	breast:
10	chr14:68952706..68954399-chr14:69260953..69263040,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11158737	1.00[JPT][hapmap]
rs11158742	1.00[JPT][hapmap]
rs12435006	1.00[JPT][hapmap]
rs12588330	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12889206	0.85[MEX][hapmap]
rs12897307	1.00[JPT][hapmap]
rs17755674	1.00[JPT][hapmap]
rs1956538	1.00[JPT][hapmap]
rs2064910	1.00[JPT][hapmap]
rs2331703	1.00[CHD][hapmap];0.85[MEX][hapmap]
rs2331704	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs2525507	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2753403	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2842320	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]
rs3784118	1.00[JPT][hapmap]
rs3966077	1.00[JPT][hapmap]
rs4899241	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4902571	0.85[MEX][hapmap]
rs4902578	1.00[JPT][hapmap]
rs4902580	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4902581	1.00[JPT][hapmap]
rs4902587	1.00[JPT][hapmap]
rs4902588	1.00[JPT][hapmap]
rs4902589	1.00[JPT][hapmap]
rs6573834	0.85[MEX][hapmap]
rs66597987	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145422	1.00[JPT][hapmap]
rs7150454	0.85[MEX][hapmap]
rs72727487	1.00[ASN][1000 genomes]
rs8003606	1.00[CHB][hapmap]
rs8009876	0.85[MEX][hapmap]
rs8010430	1.00[ASN][1000 genomes]
rs8019592	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9323510	1.00[JPT][hapmap]
rs975422	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
rs4899243	C14orf50	cis	cerebellum	SCAN
rs4899243	NCRNA00238	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68943800-68957400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:68944000-68959200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr14:68944200-68955000	Weak transcription	Esophagus	oesophagus
4	chr14:68944200-68957400	Weak transcription	Fetal Muscle Leg	muscle
5	chr14:68944400-68968200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr14:68944600-68957400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr14:68945400-68959600	Weak transcription	Primary B cells from cord blood	blood
8	chr14:68949600-68955400	Enhancers	Pancreas	Pancrea
9	chr14:68949800-68955600	Enhancers	Hela-S3	cervix
10	chr14:68950000-68954800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr14:68950200-68954600	Enhancers	HepG2	liver
12	chr14:68950600-68968200	Weak transcription	Gastric	stomach
13	chr14:68950800-68954400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr14:68950800-68954600	Weak transcription	NH-A	brain
15	chr14:68950800-68954600	Weak transcription	NHLF	lung
16	chr14:68950800-68959200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr14:68951000-68954000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:68951000-68954200	Weak transcription	Osteobl	bone
19	chr14:68951000-68954400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr14:68951000-68954400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr14:68951000-68954400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr14:68951000-68954400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr14:68951000-68954600	Weak transcription	GM12878-XiMat	blood
24	chr14:68951000-68955400	Enhancers	K562	blood
25	chr14:68951000-68957400	Weak transcription	Fetal Stomach	stomach
26	chr14:68951000-68957400	Weak transcription	Spleen	Spleen
27	chr14:68951000-68959400	Weak transcription	Fetal Kidney	kidney
28	chr14:68951000-68969400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr14:68951600-68955000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr14:68951800-68954000	Enhancers	Fetal Intestine Small	intestine
31	chr14:68951800-68960400	Weak transcription	Colon Smooth Muscle	Colon
32	chr14:68952000-68954000	Enhancers	Fetal Intestine Large	intestine
33	chr14:68952000-68954600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr14:68952000-68958600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr14:68952000-68961800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr14:68952000-68967600	Weak transcription	Thymus	Thymus
37	chr14:68952200-68954400	Weak transcription	Fetal Thymus	thymus
38	chr14:68952200-68954600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr14:68952400-68954600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr14:68952400-68960600	Weak transcription	Primary T cells from cord blood	blood
41	chr14:68952600-68954000	Enhancers	A549	lung
42	chr14:68952600-68954800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr14:68952800-68954000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr14:68953000-68954800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr14:68953200-68954000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr14:68953200-68954200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr14:68953200-68954600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr14:68953200-68960400	Weak transcription	Fetal Lung	lung
49	chr14:68953400-68960200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr14:68953600-68954000	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links