Variant report

Variant	rs599849
Chromosome Location	chr3:101576762-101576763
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	chr3:101576577..101579406-chr3:101942461..101944308,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs14134	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925332	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2925333	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2926538	0.80[ASN][1000 genomes]
rs2926539	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2926540	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2929922	0.80[ASN][1000 genomes]
rs587555	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs592332	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs592779	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs601225	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs618901	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs622122	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641432	0.80[ASN][1000 genomes]
rs654219	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs665374	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs677011	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs678354	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs680508	0.98[ASN][1000 genomes]
rs681573	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs688058	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs694293	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs694936	0.80[ASN][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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101570000-101578000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:101570000-101579200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:101570400-101598400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:101570600-101577600	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
5	chr3:101570800-101579400	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:101570800-101580600	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr3:101570800-101580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:101570800-101580800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:101570800-101580800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:101571000-101576800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:101571000-101577200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:101571000-101579400	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr3:101571000-101579400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:101571000-101579400	Strong transcription	Dnd41	blood
15	chr3:101571000-101580000	Strong transcription	Fetal Lung	lung
16	chr3:101571000-101580600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:101571000-101581400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:101571200-101579400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:101571200-101579400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:101571200-101579400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:101571200-101579400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr3:101571200-101579400	Strong transcription	Fetal Muscle Leg	muscle
23	chr3:101571200-101580600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:101571200-101580600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:101571200-101581000	Strong transcription	Colon Smooth Muscle	Colon
26	chr3:101571200-101582000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:101571400-101579600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:101571400-101580800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:101571400-101581400	Strong transcription	NHLF	lung
30	chr3:101571600-101579200	Strong transcription	Brain Cingulate Gyrus	brain
31	chr3:101571600-101580600	Strong transcription	Fetal Thymus	thymus
32	chr3:101571800-101579400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:101571800-101579400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:101572000-101577400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr3:101572000-101578800	Strong transcription	Primary B cells from cord blood	blood
36	chr3:101572200-101579200	Strong transcription	K562	blood
37	chr3:101572200-101581400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:101572600-101576800	Strong transcription	Spleen	Spleen
39	chr3:101572600-101577200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:101572600-101577600	Genic enhancers	Muscle Satellite Cultured Cells	--
41	chr3:101572600-101580400	Strong transcription	HUVEC	blood vessel
42	chr3:101572600-101581000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:101572600-101581200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:101572600-101581400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:101572600-101581800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:101572600-101583400	Strong transcription	Primary hematopoietic stem cells	blood
47	chr3:101572800-101580800	Strong transcription	HMEC	breast
48	chr3:101573000-101577600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:101573600-101579400	Strong transcription	Aorta	Aorta
50	chr3:101574200-101579600	Strong transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links