Variant report

Variant	rs11058001
Chromosome Location	chr12:122888594-122888595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr12:122888273-122888854	GM12878	blood:	n/a	n/a
2	MAX	chr12:122888537-122888712	GM12878	blood:	n/a	n/a
3	BATF	chr12:122888348-122888720	GM12878	blood:	n/a	n/a
4	WRNIP1	chr12:122888507-122888701	GM12878	blood:	n/a	n/a
5	EBF1	chr12:122888315-122888760	GM12878	blood:	n/a	n/a
6	RUNX3	chr12:122888308-122888738	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122887097..122891186-chr12:122896000..122898774,4	MCF-7	breast:
2	chr12:122887135..122888989-chr12:122893412..122896084,2	MCF-7	breast:

Variant related genes	Relation type
CLIP1	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10846839	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10846854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10846879	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10846896	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10847103	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11057562	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11057787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057801	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11057810	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11057832	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057894	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057934	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058009	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11058010	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11058043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11058062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058064	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11058099	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11058136	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11058143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11058144	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11058159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11058186	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11058206	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11058232	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11058237	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11058480	0.91[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs12227778	1.00[ASW][hapmap]
rs12229152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12229345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12424715	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12427143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12427421	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2173581	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3817012	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4758661	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4758672	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4758694	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4758697	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56861120	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56863652	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58062133	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58766840	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58853108	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61954399	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61954405	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61954416	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61954418	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61954421	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61954422	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61954424	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61954425	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61954427	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61954441	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61954442	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61954447	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61954450	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8181750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs882969	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11058001	TMED2	cis	parietal	SCAN
rs11058001	CIT	cis	cerebellum	SCAN
rs11058001	DHX37	cis	parietal	SCAN
rs11058001	TMED2	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122860600-122905000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:122862800-122895600	Weak transcription	Small Intestine	intestine
3	chr12:122863400-122897400	Weak transcription	Fetal Brain Female	brain
4	chr12:122863400-122897800	Weak transcription	Brain Substantia Nigra	brain
5	chr12:122863800-122905000	Weak transcription	Dnd41	blood
6	chr12:122884400-122889800	Weak transcription	Aorta	Aorta
7	chr12:122884600-122897600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:122884600-122905200	Weak transcription	Colonic Mucosa	Colon
9	chr12:122885200-122889000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:122885200-122890000	Weak transcription	Fetal Intestine Large	intestine
11	chr12:122885200-122890400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:122885200-122890800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:122885200-122891200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:122885200-122891200	Weak transcription	Adipose Nuclei	Adipose
15	chr12:122885200-122891200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:122885200-122891600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:122885200-122891600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:122885200-122893800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:122885200-122897800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:122885200-122897800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:122885200-122902400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:122885200-122902600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:122885200-122904600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:122885200-122905200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:122885200-122905400	Weak transcription	Fetal Thymus	thymus
26	chr12:122885200-122905400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:122885200-122906000	Weak transcription	Ovary	ovary
28	chr12:122885400-122891400	Weak transcription	Fetal Kidney	kidney
29	chr12:122885400-122891800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:122885400-122895400	Weak transcription	Fetal Lung	lung
31	chr12:122885400-122896000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:122885400-122898200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:122885400-122905000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:122885600-122890000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr12:122885600-122897000	Weak transcription	HUVEC	blood vessel
36	chr12:122885600-122897400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:122885600-122905400	Weak transcription	NH-A	brain
38	chr12:122885800-122890400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:122886000-122889000	Strong transcription	Fetal Intestine Small	intestine
40	chr12:122886000-122890200	Weak transcription	Stomach Mucosa	stomach
41	chr12:122886000-122891400	Weak transcription	HSMM	muscle
42	chr12:122886200-122888600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:122886200-122890400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:122886200-122890400	Weak transcription	K562	blood
45	chr12:122886200-122892000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:122886200-122892400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:122886200-122896000	Weak transcription	Right Atrium	heart
48	chr12:122886200-122897600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:122886200-122905400	Weak transcription	Right Ventricle	heart
50	chr12:122886400-122891000	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links