Variant report

Variant	rs2153140
Chromosome Location	chr6:145337401-145337402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1012099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1012100	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11155391	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890472	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1933927	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933928	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2019545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068343	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2876601	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3861403	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3966674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896769	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6570669	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6913592	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6924480	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6929370	0.95[ASN][1000 genomes]
rs7450643	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7741672	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7754511	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9376890	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390273	0.82[EUR][1000 genomes]
rs9399529	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9497171	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs951020	0.83[EUR][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	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv886742	chr6:145269757-145376903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2153140	AIG1	cis	parietal	SCAN
rs2153140	PLAGL1	cis	cerebellum	SCAN
rs2153140	HIVEP2	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145328400-145339200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:145333600-145344200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:145333800-145339200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr6:145334200-145344200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:145334600-145338600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:145335800-145337600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:145335800-145339400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:145335800-145339600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:145336000-145337600	Enhancers	A549	lung
10	chr6:145336000-145339000	Enhancers	NHDF-Ad	bronchial
11	chr6:145336000-145339000	Enhancers	Osteobl	bone
12	chr6:145336200-145337600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr6:145336200-145337800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:145336200-145338800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:145336600-145337600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:145336600-145338000	Enhancers	HUVEC	blood vessel
17	chr6:145336800-145337600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:145336800-145337600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:145336800-145337600	Enhancers	HSMM	muscle
20	chr6:145336800-145337600	Enhancers	HSMMtube	muscle
21	chr6:145336800-145337600	Enhancers	NH-A	brain
22	chr6:145336800-145337600	Enhancers	NHEK	skin
23	chr6:145336800-145338000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:145336800-145338000	Enhancers	HMEC	breast
25	chr6:145336800-145338400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:145336800-145338600	Enhancers	NHLF	lung
27	chr6:145336800-145338800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:145337000-145337600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr6:145337000-145337600	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:145337000-145338000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr6:145337200-145338600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:145337200-145344200	Weak transcription	Left Ventricle	heart
33	chr6:145337400-145337600	Enhancers	Right Atrium	heart
34	chr6:145337400-145338400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links