Variant report

Variant	rs55927797
Chromosome Location	chr11:47446292-47446293
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47443547..47446409-chr11:47561688..47563935,2	K562	blood:
2	chr11:47420268..47423188-chr11:47445332..47447348,2	K562	blood:
3	chr11:47290429..47293321-chr11:47445782..47448351,3	K562	blood:
4	chr11:47290951..47293321-chr11:47445782..47448016,2	K562	blood:

Variant related genes	Relation type
ENSG00000264583	Chromatin interaction
ENSG00000110514	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1057233	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10734557	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10742803	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769258	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10769262	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10838698	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10838699	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10838704	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838706	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838708	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10838724	0.82[ASN][1000 genomes]
rs11039199	0.84[EUR][1000 genomes]
rs11039200	0.84[EUR][1000 genomes]
rs11039202	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11039203	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11039212	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039219	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039238	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039255	0.85[ASN][1000 genomes]
rs11039265	0.80[ASN][1000 genomes]
rs11600581	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11601603	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11604680	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11605672	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11607981	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12146565	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12802273	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12803525	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1317149	0.85[ASN][1000 genomes]
rs1317164	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1542321	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2053979	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2053980	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084946	0.85[EUR][1000 genomes]
rs2293577	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293578	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293580	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2856661	0.80[AMR][1000 genomes]
rs2868459	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34958982	0.82[ASN][1000 genomes]
rs35184771	0.87[ASN][1000 genomes]
rs35496532	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35705029	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35996350	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3740686	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3781624	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781626	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781627	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752827	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4752832	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752838	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752845	0.82[ASN][1000 genomes]
rs4752987	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4752990	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752993	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4752994	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752999	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4992357	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55677087	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55876153	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56030824	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58965622	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60075622	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6485753	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6485756	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67116452	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67472071	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7105851	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7106956	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7107726	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7111957	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7124681	0.85[ASN][1000 genomes]
rs755553	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs755554	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs755555	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7924485	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7925299	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7925389	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7928163	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7928419	0.80[AMR][1000 genomes]
rs7937331	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7940536	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs896815	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs896816	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs935914	0.87[EUR][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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
8	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs55927797	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs55927797	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs55927797	C1QTNF4	cis	Muscle Skeletal	GTEx
rs55927797	SPI1	cis	multi-tissue	Pritchard
rs55927797	C1QTNF4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47431200-47447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47431600-47446400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:47432200-47446400	Strong transcription	Thymus	Thymus
4	chr11:47432400-47446400	Weak transcription	Fetal Brain Male	brain
5	chr11:47432600-47446400	Strong transcription	Fetal Brain Female	brain
6	chr11:47432800-47446400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:47435000-47446600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr11:47435200-47446400	Strong transcription	Primary T cells from cord blood	blood
9	chr11:47437400-47446400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:47437800-47446600	Strong transcription	Fetal Intestine Large	intestine
11	chr11:47438200-47446400	Weak transcription	Right Atrium	heart
12	chr11:47438200-47446600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:47438800-47446400	Strong transcription	Fetal Lung	lung
14	chr11:47439000-47446400	Strong transcription	Colonic Mucosa	Colon
15	chr11:47439000-47446600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr11:47439200-47446400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:47439200-47446400	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:47439200-47446600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:47439200-47446600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:47439200-47446600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:47439200-47446600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:47439200-47446600	Strong transcription	Colon Smooth Muscle	Colon
23	chr11:47439400-47446400	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr11:47439400-47446600	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr11:47439400-47446600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:47439400-47446600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:47439400-47446600	Strong transcription	Aorta	Aorta
28	chr11:47439400-47446600	Strong transcription	HSMMtube	muscle
29	chr11:47439600-47446600	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr11:47439600-47446600	Weak transcription	Fetal Heart	heart
31	chr11:47440000-47446400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:47440000-47446400	Strong transcription	Ovary	ovary
33	chr11:47440000-47446400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr11:47440800-47446400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:47441000-47446800	Weak transcription	Small Intestine	intestine
36	chr11:47443600-47446400	Strong transcription	Primary B cells from cord blood	blood
37	chr11:47444200-47446400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:47444400-47446600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr11:47445200-47446400	Genic enhancers	Brain Hippocampus Middle	brain
40	chr11:47445400-47446400	Genic enhancers	NHLF	lung
41	chr11:47445400-47446800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr11:47445400-47446800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr11:47445400-47446800	Genic enhancers	Right Ventricle	heart
44	chr11:47445400-47447000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:47445400-47447000	Genic enhancers	Spleen	Spleen
46	chr11:47445400-47447000	Transcr. at gene 5' and 3'	Hela-S3	cervix
47	chr11:47445600-47446400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr11:47445600-47446400	Genic enhancers	Lung	lung
49	chr11:47445600-47446400	Genic enhancers	K562	blood
50	chr11:47445600-47446800	Genic enhancers	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links