Variant report

Variant	rs925446
Chromosome Location	chr1:220472001-220472002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:220469913..220472006-chr1:220498061..220500308,2	MCF-7	breast:
2	chr1:220471708..220473237-chr1:220473384..220475197,2	K562	blood:
3	chr1:220444172..220447229-chr1:220471859..220475083,5	K562	blood:
4	chr1:220466641..220469132-chr1:220471949..220474218,2	K562	blood:

Variant related genes	Relation type
ENSG00000118873	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10863542	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863543	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10863545	0.83[AMR][1000 genomes]
rs11118518	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11589736	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1511697	0.84[AMR][1000 genomes]
rs1983247	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983248	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2089861	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2089862	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4846623	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4846627	0.84[AMR][1000 genomes]
rs756245	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs879449	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907414	0.84[AMR][1000 genomes]
rs925447	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220464200-220473600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr1:220464600-220473800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:220465200-220472600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:220467400-220472200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:220468400-220473600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:220468600-220473400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:220468600-220473400	Weak transcription	NH-A	brain
8	chr1:220468600-220473600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:220468600-220473600	Weak transcription	Fetal Stomach	stomach
10	chr1:220469200-220473400	Weak transcription	NHDF-Ad	bronchial
11	chr1:220470000-220472200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:220470800-220473400	Weak transcription	Osteobl	bone
13	chr1:220470800-220473600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:220471200-220472800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:220471200-220473200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:220471200-220473800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:220471400-220473000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:220471400-220473600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:220471600-220472400	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:220471600-220472600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr1:220471600-220472600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:220471600-220472600	Enhancers	Brain Germinal Matrix	brain
23	chr1:220471600-220473800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:220471600-220474000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr1:220471800-220472200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:220471800-220472600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:220471800-220472600	Enhancers	Adipose Nuclei	Adipose
28	chr1:220471800-220472800	Enhancers	Fetal Brain Male	brain
29	chr1:220472000-220472600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:220472000-220472600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr1:220472000-220472800	Enhancers	Fetal Brain Female	brain
32	chr1:220472000-220473600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links