Variant report

Variant	rs5950
Chromosome Location	chr4:79531202-79531203
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:79530033..79532299-chr4:79783489..79785388,2	K562	blood:
2	chr4:79531023..79534724-chr4:79692809..79696400,3	K562	blood:
3	chr4:79530799..79532363-chr4:79783489..79785979,2	K562	blood:
4	chr4:79527982..79531762-chr4:79696305..79699139,4	MCF-7	breast:
5	chr4:79526850..79529113-chr4:79529739..79531752,2	K562	blood:
6	chr4:79517123..79521487-chr4:79529586..79533380,5	K562	blood:
7	chr4:79530292..79533218-chr4:79611643..79613326,2	K562	blood:
8	chr4:79527750..79532040-chr4:79547937..79551505,3	K562	blood:
9	chr4:79529076..79531360-chr4:79643005..79644726,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000138772	Chromatin interaction
ENSG00000138756	Chromatin interaction
ENSG00000260278	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1042515	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725235	0.82[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs11727844	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11728517	0.86[ASN][1000 genomes]
rs12640075	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17003396	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628566	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4382063	0.88[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap]
rs56023152	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57415147	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57896096	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58089913	0.84[ASN][1000 genomes]
rs59133103	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5942	0.83[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs67280698	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817792	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6819559	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6836185	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837823	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72607862	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607863	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607864	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607865	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72607866	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7661370	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.84[LWK][hapmap];0.91[MKK][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7668240	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7672903	0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs7686273	0.87[CHB][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7694152	0.82[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][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	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5950	RP11-792D21.2	cis	Whole Blood	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79490800-79532600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:79491200-79535400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:79491800-79533200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:79491800-79542600	Weak transcription	NH-A	brain
5	chr4:79492000-79531600	Strong transcription	HMEC	breast
6	chr4:79502400-79532200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr4:79508200-79533600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:79512600-79534200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:79512600-79536800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:79513800-79534200	Strong transcription	NHEK	skin
11	chr4:79517200-79534800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:79518000-79548000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:79518600-79543600	Weak transcription	Stomach Mucosa	stomach
14	chr4:79521400-79534000	Weak transcription	Right Ventricle	heart
15	chr4:79522600-79531600	Weak transcription	HSMMtube	muscle
16	chr4:79523600-79533800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:79524200-79543400	Weak transcription	A549	lung
18	chr4:79524400-79532000	Weak transcription	Pancreas	Pancrea
19	chr4:79524400-79534000	Weak transcription	Placenta	Placenta
20	chr4:79525600-79531600	Weak transcription	Thymus	Thymus
21	chr4:79527800-79533200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:79527800-79533800	Weak transcription	Fetal Stomach	stomach
23	chr4:79527800-79534000	Weak transcription	Spleen	Spleen
24	chr4:79527800-79534800	Weak transcription	Gastric	stomach
25	chr4:79527800-79535200	Weak transcription	Left Ventricle	heart
26	chr4:79527800-79535200	Weak transcription	Lung	lung
27	chr4:79527800-79535400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:79527800-79542600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:79527800-79542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:79528000-79534800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:79528400-79534800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:79528600-79532000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:79528800-79531600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:79528800-79534000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr4:79529000-79532000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:79529200-79533800	Weak transcription	Fetal Intestine Small	intestine
37	chr4:79529400-79537600	Enhancers	Dnd41	blood
38	chr4:79529600-79531600	Enhancers	K562	blood
39	chr4:79529800-79536200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr4:79529800-79537000	Enhancers	Primary hematopoietic stem cells	blood
41	chr4:79530000-79533000	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr4:79530000-79540000	Enhancers	Primary T cells from cord blood	blood
43	chr4:79530400-79531400	Strong transcription	Hela-S3	cervix
44	chr4:79530800-79533800	Weak transcription	Fetal Heart	heart
45	chr4:79531000-79532400	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr4:79531000-79532800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr4:79531000-79533000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr4:79531000-79533200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr4:79531000-79535400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr4:79531200-79531400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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