Variant report

Variant	rs57415147
Chromosome Location	chr4:79535193-79535194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79534997..79539335-chr4:79548255..79551176,6	K562	blood:
2	chr4:79533816..79536159-chr4:79571823..79573589,2	K562	blood:
3	chr4:79534869..79536499-chr4:79696257..79698804,3	MCF-7	breast:
4	chr4:79531270..79533503-chr4:79534064..79536623,2	MCF-7	breast:
5	chr4:79534010..79538453-chr4:79546769..79551125,4	K562	blood:
6	chr4:79508043..79510860-chr4:79533218..79535822,2	K562	blood:
7	chr4:79534658..79536722-chr4:79591597..79593371,2	K562	blood:

Variant related genes	Relation type
ENSG00000138756	Chromatin interaction
ENSG00000260278	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1042515	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725235	0.84[ASN][1000 genomes]
rs11727844	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11728517	0.86[ASN][1000 genomes]
rs12640075	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17003396	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628566	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56023152	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57896096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58089913	0.84[ASN][1000 genomes]
rs59133103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5942	0.83[ASN][1000 genomes]
rs5950	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67280698	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817792	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6819559	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6836185	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837823	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72607862	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607863	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607864	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607865	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72607866	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7661370	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7668240	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7672903	0.84[ASN][1000 genomes]
rs7686273	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7694152	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
rs57415147	RP11-792D21.2	cis	Whole Blood	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79491200-79535400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:79491800-79542600	Weak transcription	NH-A	brain
3	chr4:79512600-79536800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:79518000-79548000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:79518600-79543600	Weak transcription	Stomach Mucosa	stomach
6	chr4:79524200-79543400	Weak transcription	A549	lung
7	chr4:79527800-79535200	Weak transcription	Left Ventricle	heart
8	chr4:79527800-79535200	Weak transcription	Lung	lung
9	chr4:79527800-79535400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:79527800-79542600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:79527800-79542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:79529400-79537600	Enhancers	Dnd41	blood
13	chr4:79529800-79536200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr4:79529800-79537000	Enhancers	Primary hematopoietic stem cells	blood
15	chr4:79530000-79540000	Enhancers	Primary T cells from cord blood	blood
16	chr4:79531000-79535400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr4:79531200-79536600	Enhancers	Primary B cells from cord blood	blood
18	chr4:79531200-79536800	Enhancers	Primary B cells from peripheral blood	blood
19	chr4:79531400-79543000	Weak transcription	Hela-S3	cervix
20	chr4:79531800-79543200	Weak transcription	HUVEC	blood vessel
21	chr4:79532000-79536800	Enhancers	Fetal Thymus	thymus
22	chr4:79532000-79537200	Weak transcription	HSMM	muscle
23	chr4:79532200-79535200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:79532400-79536800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:79532400-79537200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:79532400-79537200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:79532600-79535200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:79532600-79537200	Weak transcription	NHDF-Ad	bronchial
29	chr4:79533000-79536200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr4:79533200-79535200	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:79533200-79536800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:79533600-79535400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr4:79533800-79535400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr4:79533800-79535400	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr4:79533800-79538600	Enhancers	Fetal Intestine Large	intestine
36	chr4:79533800-79541000	Enhancers	Fetal Intestine Small	intestine
37	chr4:79533800-79548800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:79534000-79535200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:79534000-79535400	Enhancers	Primary T cells fromperipheralblood	blood
40	chr4:79534000-79535600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr4:79534200-79535200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr4:79534200-79537200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:79534200-79537200	Weak transcription	HMEC	breast
44	chr4:79534200-79537200	Weak transcription	NHEK	skin
45	chr4:79534400-79535400	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr4:79534600-79535200	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr4:79534600-79535200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr4:79534600-79535200	Enhancers	Spleen	Spleen
49	chr4:79534600-79535200	Flanking Active TSS	K562	blood
50	chr4:79534600-79535400	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links