Variant report

Variant	rs11209952
Chromosome Location	chr1:72837500-72837501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10789336	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209948	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11209951	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584611	0.81[CHB][hapmap]
rs1380995	0.81[CHB][hapmap]
rs1432639	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1460942	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1460943	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1776012	0.81[CHB][hapmap]
rs1841499	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568958	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs2568960	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568961	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2613494	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815752	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815753	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3101336	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs3101340	0.81[CHB][hapmap]
rs9424977	0.81[CHB][hapmap]
rs990871	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428454	chr1:72504469-72926256	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	esv2757734	chr1:72742396-72886813	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2758939	chr1:72742396-72886813	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3491557	chr1:72742853-72851634	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3491558	chr1:72742853-72851634	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv830204	chr1:72749851-72938571	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3584809	chr1:72768936-72844844	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
8	nsv947113	chr1:72810737-72948614	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv2422432	chr1:72821856-73148651	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11209952	RP11-292O17.1	cis	Thyroid	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72834800-72837800	Enhancers	Dnd41	blood
2	chr1:72835600-72840000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:72836200-72837600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:72836800-72837800	Enhancers	HMEC	breast
5	chr1:72836800-72838000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:72837000-72837600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:72837000-72837600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:72837000-72837600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:72837000-72837600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:72837000-72837600	Enhancers	Fetal Muscle Leg	muscle
11	chr1:72837000-72837800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:72837000-72837800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:72837000-72837800	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr1:72837000-72837800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:72837000-72837800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:72837200-72837600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr1:72837200-72837600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:72837200-72837600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:72837200-72837600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:72837200-72837800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr1:72837200-72837800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:72837200-72837800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:72837200-72837800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr1:72837200-72837800	Enhancers	Fetal Thymus	thymus
25	chr1:72837200-72837800	Enhancers	NHEK	skin
26	chr1:72837200-72838000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:72837200-72838000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:72837400-72837800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:72837400-72837800	Enhancers	H9 Cell Line	embryonic stem cell
30	chr1:72837400-72837800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:72837400-72837800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:72837400-72837800	Enhancers	Hela-S3	cervix
33	chr1:72837400-72838000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links