Variant report

Variant	rs6485756
Chromosome Location	chr11:47434777-47434778
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	POLR2A	chr11:47434770-47441206	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:47434444-47434879	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47391440..47404809-chr11:47427075..47436409,23	K562	blood:
2	chr11:47236484..47238469-chr11:47432322..47435260,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255197	TF binding region
SLC39A13	TF binding region
ENSG00000134574	Chromatin interaction
ENSG00000066336	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10742803	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10769258	0.83[EUR][1000 genomes]
rs10769262	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10838698	0.82[EUR][1000 genomes]
rs10838699	0.82[EUR][1000 genomes]
rs10838704	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838706	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039203	0.82[EUR][1000 genomes]
rs11039212	0.82[EUR][1000 genomes]
rs11039219	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11600581	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11601603	0.82[EUR][1000 genomes]
rs11604680	0.83[ASN][1000 genomes]
rs11605672	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11607981	0.82[EUR][1000 genomes]
rs12802273	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12803525	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1317164	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2053979	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2053980	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293577	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2293578	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293580	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2868459	0.85[ASN][1000 genomes]
rs35496532	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35705029	0.81[ASN][1000 genomes]
rs35996350	0.81[EUR][1000 genomes]
rs3781624	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3781625	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3781626	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3781627	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4752827	0.83[EUR][1000 genomes]
rs4752832	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752838	0.82[ASN][1000 genomes]
rs4752987	0.81[EUR][1000 genomes]
rs4752990	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4752993	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4752994	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4752999	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4992357	0.83[EUR][1000 genomes]
rs55677087	0.82[EUR][1000 genomes]
rs55876153	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55927797	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58965622	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60075622	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6485753	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67116452	0.82[EUR][1000 genomes]
rs67472071	0.81[EUR][1000 genomes]
rs7105851	0.82[EUR][1000 genomes]
rs7106956	0.82[ASN][1000 genomes]
rs7107726	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111957	0.85[EUR][1000 genomes]
rs755553	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs755554	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs755555	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7924485	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7925299	0.84[ASN][1000 genomes]
rs7925389	0.81[ASN][1000 genomes]
rs7928163	0.82[EUR][1000 genomes]
rs7937331	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7940536	0.83[EUR][1000 genomes]
rs896815	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs896816	0.83[EUR][1000 genomes]
rs935914	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv541034	chr11:47404083-47440081	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
9	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
10	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6485756	C1QTNF4	cis	Muscle Skeletal	GTEx
rs6485756	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs6485756	C1QTNF4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47431000-47435000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr11:47431000-47435400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr11:47431000-47435400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:47431000-47439200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:47431000-47440000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:47431000-47442000	Weak transcription	Primary B cells from cord blood	blood
7	chr11:47431200-47435000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr11:47431200-47435200	Weak transcription	Primary T cells from cord blood	blood
9	chr11:47431200-47435400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:47431200-47435400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:47431200-47435600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:47431200-47437600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:47431200-47439000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr11:47431200-47439800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr11:47431200-47440600	Weak transcription	Small Intestine	intestine
16	chr11:47431200-47447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr11:47431400-47434800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:47431400-47435000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr11:47431400-47435000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:47431400-47435200	Weak transcription	Liver	Liver
21	chr11:47431400-47436600	Weak transcription	Psoas Muscle	Psoas
22	chr11:47431400-47440400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr11:47431600-47434800	Weak transcription	Aorta	Aorta
24	chr11:47431600-47435000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:47431600-47435000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:47431600-47435400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:47431600-47437400	Strong transcription	Fetal Intestine Small	intestine
28	chr11:47431600-47437800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:47431600-47439000	Weak transcription	K562	blood
30	chr11:47431600-47439600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:47431600-47439800	Weak transcription	GM12878-XiMat	blood
32	chr11:47431600-47440200	Genic enhancers	Right Ventricle	heart
33	chr11:47431600-47440400	Weak transcription	Fetal Kidney	kidney
34	chr11:47431600-47446400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:47431800-47435200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:47431800-47437000	Weak transcription	Right Atrium	heart
37	chr11:47431800-47438800	Genic enhancers	Fetal Muscle Leg	muscle
38	chr11:47431800-47440400	Genic enhancers	Placenta	Placenta
39	chr11:47431800-47440800	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr11:47432000-47437200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:47432000-47437400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr11:47432200-47435000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:47432200-47435000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr11:47432200-47435000	Weak transcription	Adipose Nuclei	Adipose
45	chr11:47432200-47435000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:47432200-47435800	Weak transcription	Fetal Heart	heart
47	chr11:47432200-47436200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:47432200-47437200	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:47432200-47438600	Genic enhancers	HMEC	breast
50	chr11:47432200-47446400	Strong transcription	Thymus	Thymus

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