Variant report

Variant	rs28379646
Chromosome Location	chr4:89973621-89973622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:89962640..89965457-chr4:89973321..89975706,2	K562	blood:
2	chr4:89970076..89973919-chr4:89975021..89978811,7	K562	blood:
3	chr4:89963957..89965462-chr4:89973010..89975706,2	K562	blood:

Variant related genes	Relation type
ENSG00000138640	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10024807	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10027874	0.83[AMR][1000 genomes]
rs10029662	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10030342	0.83[AMR][1000 genomes]
rs11097209	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097210	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097211	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13140085	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13150503	0.83[AMR][1000 genomes]
rs17014898	0.91[ASN][1000 genomes]
rs17014901	0.91[ASN][1000 genomes]
rs17014988	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2056012	0.85[AMR][1000 genomes]
rs34378169	0.87[ASN][1000 genomes]
rs34693890	0.91[ASN][1000 genomes]
rs36048928	0.91[ASN][1000 genomes]
rs59385067	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61286299	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532102	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67317338	0.91[ASN][1000 genomes]
rs6823660	0.81[AMR][1000 genomes]
rs6826407	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6827398	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6853075	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6857969	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7660377	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7668782	0.81[AMR][1000 genomes]
rs7674344	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs874147	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9992522	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9996559	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89937200-89975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:89944200-89978000	Weak transcription	Pancreas	Pancrea
3	chr4:89958200-89974400	Weak transcription	Aorta	Aorta
4	chr4:89959000-89975400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:89959200-89974400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:89963200-89975800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:89970600-89975200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:89971000-89974000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:89971200-89974400	Weak transcription	HUVEC	blood vessel
10	chr4:89971600-89974400	Weak transcription	K562	blood
11	chr4:89972600-89975400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr4:89972600-89975400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr4:89973000-89974400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:89973000-89975800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:89973200-89974200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:89973200-89974200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:89973200-89975000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:89973200-89975600	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:89973200-89977000	Weak transcription	Psoas Muscle	Psoas
20	chr4:89973400-89974000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:89973400-89974600	Weak transcription	Ovary	ovary
22	chr4:89973400-89975200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:89973400-89976400	Weak transcription	Fetal Intestine Small	intestine
24	chr4:89973400-89976800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:89973400-89977800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:89973400-89977800	Weak transcription	Right Ventricle	heart
27	chr4:89973600-89974000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:89973600-89975600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr4:89973600-89977800	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links