Variant report

Variant	rs28860567
Chromosome Location	chr4:8489615-8489616
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65304873..65306373-chr4:8489178..8490772,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142186	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10009196	1.00[AMR][1000 genomes]
rs10011431	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10019143	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10022276	1.00[AMR][1000 genomes]
rs13434523	1.00[AMR][1000 genomes]
rs28416714	1.00[AMR][1000 genomes]
rs28527486	1.00[AMR][1000 genomes]
rs28591490	1.00[AMR][1000 genomes]
rs28609497	1.00[AMR][1000 genomes]
rs28621881	1.00[AMR][1000 genomes]
rs28647609	1.00[AMR][1000 genomes]
rs28707116	1.00[AMR][1000 genomes]
rs28839770	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28877981	1.00[AMR][1000 genomes]
rs7695149	1.00[AMR][1000 genomes]
rs9884532	1.00[AMR][1000 genomes]
rs9985915	1.00[AMR][1000 genomes]
rs9985917	1.00[AMR][1000 genomes]
rs9986108	1.00[AMR][1000 genomes]
rs9992927	1.00[AMR][1000 genomes]
rs9997393	1.00[AMR][1000 genomes]
rs9997800	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8473600-8501400	Weak transcription	Brain Substantia Nigra	brain
2	chr4:8475600-8491400	Weak transcription	Aorta	Aorta
3	chr4:8475800-8491800	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:8478000-8500200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:8478200-8491400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:8478600-8490400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:8478600-8492000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:8479200-8501400	Weak transcription	Liver	Liver
9	chr4:8479400-8491200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:8479600-8490800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr4:8479600-8490800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:8479800-8494600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:8480000-8493000	Weak transcription	Gastric	stomach
14	chr4:8480200-8498400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:8480200-8501400	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:8480600-8498200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:8480800-8497400	Weak transcription	Spleen	Spleen
18	chr4:8481400-8490400	Weak transcription	Fetal Brain Female	brain
19	chr4:8481400-8490400	Weak transcription	Lung	lung
20	chr4:8481400-8490400	Weak transcription	Ovary	ovary
21	chr4:8481400-8491800	Weak transcription	Esophagus	oesophagus
22	chr4:8481400-8495200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:8481400-8496800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:8481400-8501400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:8481600-8493200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:8481800-8490600	Weak transcription	Fetal Stomach	stomach
27	chr4:8481800-8491800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:8481800-8497400	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:8482200-8495000	Weak transcription	Brain Germinal Matrix	brain
30	chr4:8482200-8501400	Weak transcription	Primary T cells from cord blood	blood
31	chr4:8483800-8494400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:8484200-8497000	Weak transcription	Placenta	Placenta
33	chr4:8488000-8490800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:8488800-8490400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:8489000-8492200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:8489200-8490600	Weak transcription	K562	blood

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