Variant report

Variant	rs55962013
Chromosome Location	chr11:77628968-77628969
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	USF1	chr11:77628756-77629143	A549	lung:	n/a	n/a
2	SPI1	chr11:77628943-77629097	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000255115	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11237326	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11237328	0.86[EUR][1000 genomes]
rs11237329	0.86[EUR][1000 genomes]
rs11237335	0.81[EUR][1000 genomes]
rs11237338	0.82[EUR][1000 genomes]
rs11237341	0.83[EUR][1000 genomes]
rs11237347	0.82[EUR][1000 genomes]
rs11501934	0.81[EUR][1000 genomes]
rs11600140	0.80[AFR][1000 genomes]
rs11605955	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11606549	0.80[AFR][1000 genomes]
rs11606971	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11607032	0.80[AFR][1000 genomes]
rs11607479	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11607512	0.82[EUR][1000 genomes]
rs12273552	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12279880	0.84[EUR][1000 genomes]
rs12284929	0.85[EUR][1000 genomes]
rs12289316	0.82[EUR][1000 genomes]
rs12292039	0.84[EUR][1000 genomes]
rs12293597	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12799701	0.82[EUR][1000 genomes]
rs13377546	0.82[EUR][1000 genomes]
rs17752458	0.82[EUR][1000 genomes]
rs17825404	0.82[EUR][1000 genomes]
rs1823507	0.81[EUR][1000 genomes]
rs2305317	0.81[EUR][1000 genomes]
rs4123593	0.81[EUR][1000 genomes]
rs4123595	0.81[EUR][1000 genomes]
rs55878159	0.83[EUR][1000 genomes]
rs57055061	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7115801	0.84[EUR][1000 genomes]
rs7119720	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7131359	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72939500	0.81[EUR][1000 genomes]
rs72941339	0.81[EUR][1000 genomes]
rs72941353	0.82[EUR][1000 genomes]
rs9630225	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv975205	chr11:77628075-77671380	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55962013	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77577400-77630800	Weak transcription	Fetal Heart	heart
2	chr11:77583400-77670600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
4	chr11:77591800-77650400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
6	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr11:77597600-77629400	Weak transcription	Brain Germinal Matrix	brain
8	chr11:77597800-77629000	Weak transcription	Aorta	Aorta
9	chr11:77597800-77633800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:77597800-77644200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:77597800-77644400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:77597800-77669800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:77597800-77671000	Weak transcription	Fetal Brain Male	brain
14	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
17	chr11:77597800-77690000	Weak transcription	Gastric	stomach
18	chr11:77601800-77629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr11:77602000-77640600	Weak transcription	K562	blood
20	chr11:77602600-77644200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr11:77603000-77637400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:77603200-77650200	Weak transcription	Fetal Brain Female	brain
24	chr11:77604800-77644200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:77612600-77637000	Weak transcription	Brain Anterior Caudate	brain
26	chr11:77614600-77629200	Weak transcription	Lung	lung
27	chr11:77614800-77638800	Weak transcription	Brain Angular Gyrus	brain
28	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
29	chr11:77615000-77644200	Weak transcription	Spleen	Spleen
30	chr11:77615000-77656400	Weak transcription	Right Ventricle	heart
31	chr11:77615200-77637400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:77618200-77668200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr11:77618400-77629000	Weak transcription	Left Ventricle	heart
34	chr11:77618800-77629000	Weak transcription	Fetal Muscle Leg	muscle
35	chr11:77618800-77635000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:77618800-77637200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr11:77618800-77644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr11:77619000-77636600	Weak transcription	Placenta	Placenta
39	chr11:77619000-77667000	Weak transcription	Fetal Kidney	kidney
40	chr11:77619000-77668000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:77619200-77637200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:77619200-77637400	Weak transcription	GM12878-XiMat	blood
43	chr11:77620800-77642000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:77621800-77631200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr11:77622200-77630200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:77622200-77635600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:77622600-77636800	Weak transcription	Primary B cells from cord blood	blood
48	chr11:77622800-77634000	Weak transcription	Fetal Intestine Large	intestine
49	chr11:77625000-77630200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr11:77625000-77630400	Strong transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links