Variant report

Variant	rs55677087
Chromosome Location	chr11:47397714-47397715
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47397121..47400538-chr11:47420513..47424481,4	K562	blood:
2	chr11:47278014..47279566-chr11:47397375..47399995,2	K562	blood:
3	chr11:47395359..47404298-chr11:47408556..47417905,22	K562	blood:
4	chr11:47397140..47399846-chr11:47404698..47406803,2	MCF-7	breast:
5	chr11:47394067..47402014-chr11:47426765..47432976,19	K562	blood:
6	chr11:47395793..47399291-chr11:47428329..47431622,5	MCF-7	breast:
7	chr11:47289554..47292260-chr11:47397624..47400665,3	K562	blood:
8	chr11:47199421..47202376-chr11:47396791..47399041,2	K562	blood:
9	chr11:47391440..47404809-chr11:47427075..47436409,23	K562	blood:
10	chr11:47392669..47398633-chr11:47427643..47432695,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000165912	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000255197	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000264583	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1057233	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10734557	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10742803	0.90[EUR][1000 genomes]
rs10769258	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769262	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838698	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838699	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10838704	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10838706	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11039195	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039199	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11039200	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039202	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039203	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039212	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039219	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11600581	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11601603	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11604680	0.81[EUR][1000 genomes]
rs11605672	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11607981	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12146565	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12802273	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12803525	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1317164	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1542321	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2053979	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2053980	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2071304	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2084946	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2293577	0.90[EUR][1000 genomes]
rs2293578	0.89[EUR][1000 genomes]
rs2293580	0.89[EUR][1000 genomes]
rs2856661	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2868459	0.81[EUR][1000 genomes]
rs35496532	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35705029	0.81[EUR][1000 genomes]
rs35996350	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3740686	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3781624	0.88[EUR][1000 genomes]
rs3781625	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3781626	0.89[EUR][1000 genomes]
rs3781627	0.82[EUR][1000 genomes]
rs4752827	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752832	0.80[EUR][1000 genomes]
rs4752987	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752990	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752993	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752994	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752999	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4992357	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55876153	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55927797	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56030824	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58965622	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60075622	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6485753	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6485756	0.82[EUR][1000 genomes]
rs67116452	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67472071	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7105851	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7107726	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7111957	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs755553	0.90[EUR][1000 genomes]
rs755554	0.90[EUR][1000 genomes]
rs755555	0.90[EUR][1000 genomes]
rs7924485	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7928163	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7928419	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7937331	0.90[EUR][1000 genomes]
rs7940536	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs896815	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs896816	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs935914	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs55677087	C1QTNF4	cis	Muscle Skeletal	GTEx
rs55677087	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs55677087	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs55677087	SPI1	cis	multi-tissue	Pritchard
rs55677087	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs55677087	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47377200-47397800	Weak transcription	Fetal Muscle Leg	muscle
2	chr11:47377600-47397800	Weak transcription	Brain Substantia Nigra	brain
3	chr11:47380000-47397800	Weak transcription	Esophagus	oesophagus
4	chr11:47380200-47397800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:47390200-47398400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr11:47393200-47399600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:47395200-47398000	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
8	chr11:47395200-47398000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
9	chr11:47395200-47410000	Weak transcription	Gastric	stomach
10	chr11:47395400-47397800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr11:47395400-47397800	Enhancers	K562	blood
12	chr11:47395400-47398000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
13	chr11:47395600-47397800	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
14	chr11:47395600-47397800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:47395600-47398400	Weak transcription	Fetal Stomach	stomach
16	chr11:47395600-47399200	Weak transcription	Brain Angular Gyrus	brain
17	chr11:47395800-47397800	Weak transcription	Fetal Intestine Small	intestine
18	chr11:47395800-47398600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:47396000-47398400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr11:47396000-47398600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:47396200-47397800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr11:47396200-47398800	Weak transcription	Thymus	Thymus
23	chr11:47396200-47399200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr11:47396200-47399600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr11:47396400-47397800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:47396400-47397800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:47396400-47398000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:47396400-47398000	Weak transcription	A549	lung
29	chr11:47396400-47398200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:47396400-47398200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:47396400-47398400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr11:47396400-47398600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:47396400-47400000	Active TSS	Brain Hippocampus Middle	brain
34	chr11:47396600-47397800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:47396600-47397800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
36	chr11:47396600-47398200	Weak transcription	NHEK	skin
37	chr11:47396600-47400400	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr11:47396800-47398200	Weak transcription	HMEC	breast
39	chr11:47396800-47400400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr11:47397000-47398800	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr11:47397000-47399200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:47397000-47400400	Active TSS	Placenta	Placenta
43	chr11:47397200-47397800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr11:47397200-47398000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:47397200-47400000	Active TSS	Stomach Smooth Muscle	stomach
46	chr11:47397200-47400800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:47397400-47397800	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
48	chr11:47397400-47398200	Flanking Active TSS	GM12878-XiMat	blood
49	chr11:47397400-47400400	Active TSS	Colonic Mucosa	Colon
50	chr11:47397400-47401200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links