Variant report

Variant	rs2700473
Chromosome Location	chr3:150878284-150878285
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	chr3:150871697..150875423-chr3:150878155..150880928,3	K562	blood:
2	chr3:150873170..150876037-chr3:150877057..150879600,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10513390	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs1220996	0.91[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1221001	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1221005	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1231521	1.00[YRI][hapmap]
rs12497969	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12634353	0.82[CEU][hapmap]
rs1554121	0.82[ASW][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs2048229	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs2116290	1.00[YRI][hapmap]
rs2567322	0.91[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2700471	0.83[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2700474	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35995638	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60312353	0.80[EUR][1000 genomes]
rs7629773	0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs891666	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs977423	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9942131	0.90[CHB][hapmap];0.89[JPT][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	nsv829756	chr3:150692636-150889738	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv877648	chr3:150792444-150895145	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150863200-150889000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:150865000-150886400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:150868800-150887400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:150871200-150888400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:150872200-150881800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:150872800-150910800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:150873200-150881600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:150873200-150884000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:150873200-150887000	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:150873200-150888800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:150873200-150910200	Weak transcription	Brain Angular Gyrus	brain
12	chr3:150873400-150879800	Weak transcription	Fetal Brain Male	brain
13	chr3:150873600-150889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:150873800-150890000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:150873800-150890000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:150873800-150913800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:150874200-150888600	Weak transcription	Brain Anterior Caudate	brain
18	chr3:150874200-150888800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:150874200-150896000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:150874600-150886200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:150874600-150888400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:150874600-150889200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:150874800-150880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:150874800-150900200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:150876400-150878400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:150876400-150878400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:150877000-150880400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:150877000-150883200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:150877600-150888800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:150878000-150878600	Enhancers	HepG2	liver
31	chr3:150878000-150879000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:150878000-150888400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:150878000-150946000	Weak transcription	Placenta	Placenta
34	chr3:150878200-150878400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:150878200-150878600	Enhancers	Duodenum Mucosa	Duodenum
36	chr3:150878200-150879200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:150878200-150879400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:150878200-150883200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links