Variant report

Variant	rs3758675
Chromosome Location	chr11:47400602-47400603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47399102-47400831	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:47399086-47401154	GM12878	blood:	n/a	n/a
3	ELF1	chr11:47399876-47400686	K562	blood:	n/a	n/a
4	POLR2A	chr11:47399422-47400779	K562	blood:	n/a	n/a
5	POLR2A	chr11:47399120-47400915	Raji	blood:	n/a	n/a
6	EBF1	chr11:47399939-47400782	GM12878	blood:	n/a	chr11:47400126-47400137
7	POLR2A	chr11:47398188-47400675	GM12878	blood:	n/a	n/a
8	STAT5A	chr11:47399187-47400662	GM12878	blood:	n/a	chr11:47400185-47400192 chr11:47399731-47399739
9	TBL1XR1	chr11:47399703-47400711	K562	blood:	n/a	n/a
10	POLR2A	chr11:47398904-47400643	GM12878	blood:	n/a	n/a
11	POLR2A	chr11:47395963-47401300	HL-60	blood:	n/a	n/a
12	POLR2A	chr11:47399186-47400625	GM18505	blood:	n/a	n/a
13	POLR2A	chr11:47397663-47400732	K562	blood:	n/a	n/a
14	PML	chr11:47399365-47400605	GM12878	blood:	n/a	n/a
15	POLR2A	chr11:47397376-47401224	GM12878	blood:	n/a	n/a
16	GATA1	chr11:47397923-47401398	K562	blood:	n/a	n/a
17	POLR2A	chr11:47398225-47400774	GM12892	blood:	n/a	n/a
18	POLR2A	chr11:47399674-47400870	GM12891	blood:	n/a	n/a
19	POLR2A	chr11:47397519-47401084	GM12892	blood:	n/a	n/a
20	POLR2A	chr11:47399658-47400603	K562	blood:	n/a	n/a
21	POLR2A	chr11:47399162-47400634	GM19193	blood:	n/a	n/a
22	POLR2A	chr11:47399522-47400879	K562	blood:	n/a	n/a
23	GATA1	chr11:47399716-47400615	PBDE	blood:	n/a	n/a
24	POLR2A	chr11:47398272-47400728	GM12878	blood:	n/a	n/a
25	POLR2A	chr11:47397855-47400670	K562	blood:	n/a	n/a
26	CHD2	chr11:47399637-47400897	GM12878	blood:	n/a	n/a
27	WRNIP1	chr11:47399895-47400821	GM12878	blood:	n/a	n/a
28	POLR2A	chr11:47395858-47401398	HL-60	blood:	n/a	n/a
29	NR2F2	chr11:47399047-47400788	K562	blood:	n/a	n/a
30	CBX3	chr11:47399543-47400795	K562	blood:	n/a	n/a
31	MTA3	chr11:47397662-47400909	GM12878	blood:	n/a	n/a
32	HEY1	chr11:47399614-47400671	K562	blood:	n/a	n/a
33	ZBTB7A	chr11:47398839-47400609	K562	blood:	n/a	n/a
34	JUN	chr11:47397764-47401060	K562	blood:	n/a	chr11:47398988-47398999 chr11:47400136-47400145
35	ELF1	chr11:47398377-47400632	GM12878	blood:	n/a	chr11:47399580-47399592
36	ZMIZ1	chr11:47399762-47400655	K562	blood:	n/a	n/a
37	POLR2A	chr11:47399552-47400822	GM12892	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47395359..47404298-chr11:47408556..47417905,22	K562	blood:
2	chr11:47394067..47402014-chr11:47426765..47432976,19	K562	blood:
3	chr11:47399997..47402556-chr8:126443816..126446707,2	MCF-7	breast:
4	chr11:47289554..47292260-chr11:47397624..47400665,3	K562	blood:
5	chr11:47399004..47400770-chr11:47446343..47448819,3	K562	blood:
6	chr11:47400529..47402179-chr11:47427161..47429791,2	MCF-7	breast:
7	chr11:47391440..47404809-chr11:47427075..47436409,23	K562	blood:
8	chr11:47400131..47402578-chr11:47411947..47414997,4	K562	blood:

No data

Variant related genes	Relation type
SPI1	TF binding region
ENSG00000165916	Chromatin interaction
ENSG00000255197	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000173334	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000025434	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10437655	0.90[EUR][1000 genomes]
rs10742802	0.82[EUR][1000 genomes]
rs10769263	0.86[EUR][1000 genomes]
rs10769264	0.83[EUR][1000 genomes]
rs10838702	0.86[EUR][1000 genomes]
rs10838705	0.83[EUR][1000 genomes]
rs11039221	0.83[EUR][1000 genomes]
rs11039225	0.83[EUR][1000 genomes]
rs11606287	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1377416	0.86[EUR][1000 genomes]
rs1534576	0.83[EUR][1000 genomes]
rs2278890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293579	0.82[EUR][1000 genomes]
rs34937994	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35032070	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3824869	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71475909	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7947450	0.83[EUR][1000 genomes]
rs874896	0.83[EUR][1000 genomes]
rs896817	0.89[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3758675	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47395200-47410000	Weak transcription	Gastric	stomach
2	chr11:47397200-47400800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr11:47397400-47401200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:47397800-47400800	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr11:47398600-47400800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr11:47399400-47404200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:47399400-47421400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:47399800-47404200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr11:47399800-47405000	Weak transcription	Right Atrium	heart
10	chr11:47399800-47405800	Weak transcription	Brain Angular Gyrus	brain
11	chr11:47399800-47421200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:47400000-47404000	Weak transcription	Lung	lung
13	chr11:47400000-47404200	Weak transcription	Adipose Nuclei	Adipose
14	chr11:47400000-47410000	Weak transcription	Brain Hippocampus Middle	brain
15	chr11:47400000-47415200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:47400000-47416000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:47400000-47416800	Weak transcription	Brain Anterior Caudate	brain
18	chr11:47400000-47421200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:47400200-47400800	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr11:47400200-47400800	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr11:47400200-47400800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr11:47400200-47400800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:47400200-47400800	Enhancers	Fetal Thymus	thymus
24	chr11:47400200-47400800	Flanking Active TSS	GM12878-XiMat	blood
25	chr11:47400200-47401000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr11:47400200-47401000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr11:47400400-47401200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr11:47400600-47401400	Enhancers	K562	blood
29	chr11:47400600-47403400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:47400600-47404000	Weak transcription	Spleen	Spleen
31	chr11:47400600-47404200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:47400600-47409800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links