Variant report

Variant	rs6014093
Chromosome Location	chr20:53250421-53250422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53249127..53250955-chr20:53263341..53265497,2	MCF-7	breast:
2	chr20:53239460..53242242-chr20:53249088..53250613,2	MCF-7	breast:
3	chr20:53250383..53253224-chr20:53254055..53257121,4	MCF-7	breast:
4	chr17:56707799..56709704-chr20:53250270..53252481,2	MCF-7	breast:
5	chr20:52824655..52827379-chr20:53249920..53251960,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs6014095	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6014097	0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6023435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6023436	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6023447	1.00[MEX][hapmap]
rs7270771	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv586282	chr20:53218978-53254815	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53242400-53270200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:53246600-53251000	Enhancers	Fetal Brain Male	brain
3	chr20:53249600-53250800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr20:53249600-53250800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr20:53249600-53252200	Enhancers	H1 Cell Line	embryonic stem cell
6	chr20:53249600-53259800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:53249800-53250600	Enhancers	H9 Cell Line	embryonic stem cell
8	chr20:53249800-53250600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr20:53249800-53250600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr20:53249800-53250600	Enhancers	Fetal Brain Female	brain
11	chr20:53249800-53250800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr20:53249800-53250800	Flanking Active TSS	GM12878-XiMat	blood
13	chr20:53249800-53251000	Enhancers	Primary B cells from peripheral blood	blood
14	chr20:53249800-53252200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr20:53250000-53250600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr20:53250000-53250800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr20:53250000-53250800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr20:53250000-53251000	Enhancers	Fetal Muscle Leg	muscle
19	chr20:53250200-53250600	Flanking Active TSS	Brain Germinal Matrix	brain
20	chr20:53250200-53250800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr20:53250200-53251000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr20:53250400-53250600	Enhancers	Psoas Muscle	Psoas
23	chr20:53250400-53250800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr20:53250400-53251000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links