Variant report

Variant	rs4469852
Chromosome Location	chr11:100633536-100633537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11224405	0.82[ASN][1000 genomes]
rs11824393	0.82[ASN][1000 genomes]
rs11824432	0.82[ASN][1000 genomes]
rs12284151	0.82[ASN][1000 genomes]
rs17095405	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095409	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095426	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];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17095428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17095429	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];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17095438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17095439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088953	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407750	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3901516	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4087602	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4121392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4337001	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4517481	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4753983	0.82[ASN][1000 genomes]
rs4754702	0.81[ASW][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap]
rs499241	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs507695	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs58727919	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60708905	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61890760	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61890763	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61890764	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61890765	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61890766	0.88[ASN][1000 genomes]
rs61892334	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61892352	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61892355	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61910476	0.88[ASN][1000 genomes]
rs61910478	0.82[ASN][1000 genomes]
rs61910480	0.82[ASN][1000 genomes]
rs61910505	0.82[ASN][1000 genomes]
rs61910508	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6590818	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7102634	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7105842	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7110872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7112228	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7112366	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7116153	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117515	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7126015	0.82[ASN][1000 genomes]
rs7126324	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130855	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003836	0.82[ASN][1000 genomes]
rs73005729	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7927197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7942588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7944598	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7945336	0.88[ASN][1000 genomes]
rs7947761	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];0.93[MEX][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][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	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4469852	TMEM123	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100621000-100642400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr11:100624600-100635000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr11:100624600-100655600	Weak transcription	Left Ventricle	heart
4	chr11:100624600-100655600	Weak transcription	Right Ventricle	heart
5	chr11:100624800-100634800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:100625000-100637600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:100626000-100639600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr11:100628200-100642800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:100629200-100642800	Weak transcription	Liver	Liver
10	chr11:100630400-100634200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:100630600-100635400	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr11:100630800-100635000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:100630800-100635200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:100630800-100635200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:100631000-100637800	Weak transcription	Placenta	Placenta
16	chr11:100631000-100639000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:100631000-100639600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr11:100631800-100635000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:100631800-100638600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:100631800-100645000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:100632000-100636000	Weak transcription	Stomach Mucosa	stomach
22	chr11:100632000-100639200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:100632000-100640000	Weak transcription	Fetal Heart	heart
24	chr11:100632200-100640000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:100632200-100645200	Weak transcription	Colonic Mucosa	Colon
26	chr11:100632200-100647200	Weak transcription	HSMM	muscle
27	chr11:100632800-100633600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr11:100632800-100635400	Weak transcription	Fetal Intestine Small	intestine
29	chr11:100632800-100639600	Weak transcription	Fetal Lung	lung
30	chr11:100632800-100645000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:100632800-100645000	Weak transcription	Gastric	stomach
32	chr11:100633000-100641600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:100633000-100647000	Weak transcription	NHLF	lung
34	chr11:100633200-100634800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:100633200-100635200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr11:100633200-100639000	Weak transcription	Small Intestine	intestine
37	chr11:100633200-100639800	Weak transcription	Adipose Nuclei	Adipose
38	chr11:100633200-100641800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:100633200-100641800	Weak transcription	Fetal Muscle Leg	muscle
40	chr11:100633200-100642600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr11:100633200-100655600	Weak transcription	Psoas Muscle	Psoas
42	chr11:100633400-100633600	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links