Variant report

Variant	rs3793999
Chromosome Location	chr11:93258844-93258845
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	MTA3	chr11:93258602-93260862	GM12878	blood:	n/a	n/a
2	IKZF1	chr11:93258745-93260241	GM12878	blood:	n/a	n/a
3	RUNX3	chr11:93258735-93260857	GM12878	blood:	n/a	n/a
4	BHLHE40	chr11:93258823-93260678	GM12878	blood:	n/a	chr11:93260246-93260262
5	PML	chr11:93258637-93260716	GM12878	blood:	n/a	chr11:93259037-93259046
6	ATF2	chr11:93258703-93260799	GM12878	blood:	n/a	n/a
7	RCOR1	chr11:93258648-93258993	GM12878	blood:	n/a	n/a
8	FOXM1	chr11:93258823-93260129	GM12878	blood:	n/a	n/a
9	NFATC1	chr11:93258798-93259404	GM12878	blood:	n/a	n/a
10	NFIC	chr11:93258744-93260146	GM12878	blood:	n/a	n/a
11	WRNIP1	chr11:93258707-93259322	GM12878	blood:	n/a	n/a
12	RUNX3	chr11:93258732-93260827	GM12878	blood:	n/a	n/a
13	BHLHE40	chr11:93258807-93259210	K562	blood:	n/a	n/a
14	MXI1	chr11:93258645-93259447	IMR90	lung:	n/a	n/a
15	REST	chr11:93258828-93259273	PFSK-1	brain:	n/a	n/a
16	BCLAF1	chr11:93258713-93260120	GM12878	blood:	n/a	n/a
17	EP300	chr11:93258843-93260664	GM12878	blood:	n/a	chr11:93259735-93259749 chr11:93259467-93259481
18	NFIC	chr11:93258725-93259991	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93256846..93259343-chr11:93261721..93264520,2	K562	blood:
2	chr11:93257690..93261836-chr11:93263663..93269980,6	K562	blood:

Variant related genes	Relation type
SMCO4	TF binding region
ENSG00000234106	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11020387	0.94[CEU][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11020388	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11020390	0.98[EUR][1000 genomes]
rs11603107	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11603540	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11603560	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11604399	0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606253	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606261	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606262	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606505	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11607585	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12789912	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790221	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12791489	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12795164	0.94[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12796609	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12806700	0.94[CEU][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12808921	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305660	0.94[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305661	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638787	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34028949	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34580908	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34819559	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35364744	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35368196	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35423935	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35901746	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35930354	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794002	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794007	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794008	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58462328	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483248	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6483249	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111773	0.88[CEU][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7130465	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71480681	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71480682	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71480685	0.90[EUR][1000 genomes]
rs7928401	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7933953	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945684	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897555	0.94[CEU][hapmap]
rs897558	1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv2760208	chr11:93172673-93266594	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3793999	SMCO4	cis	Whole Blood	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93238400-93259000	Weak transcription	Fetal Lung	lung
2	chr11:93248000-93261800	Weak transcription	Fetal Stomach	stomach
3	chr11:93249000-93261600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr11:93251000-93261400	Weak transcription	Fetal Brain Male	brain
5	chr11:93251000-93261600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:93251000-93261600	Weak transcription	Aorta	Aorta
7	chr11:93252000-93266800	Enhancers	Fetal Thymus	thymus
8	chr11:93252200-93259000	Enhancers	Liver	Liver
9	chr11:93252200-93260800	Enhancers	Dnd41	blood
10	chr11:93252600-93259800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:93253800-93266200	Weak transcription	Fetal Brain Female	brain
12	chr11:93255000-93259200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:93255000-93263600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr11:93255000-93274600	Weak transcription	Hela-S3	cervix
15	chr11:93255600-93262200	Weak transcription	Brain Germinal Matrix	brain
16	chr11:93255800-93261600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:93255800-93262000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr11:93255800-93263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:93256000-93262200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:93256200-93263800	Enhancers	Primary B cells from peripheral blood	blood
21	chr11:93256200-93266000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr11:93256400-93266600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:93256600-93259000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr11:93256600-93259400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr11:93256800-93259200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:93256800-93259800	Enhancers	Primary B cells from cord blood	blood
27	chr11:93256800-93261000	Flanking Active TSS	GM12878-XiMat	blood
28	chr11:93257000-93261000	Enhancers	Thymus	Thymus
29	chr11:93257200-93259800	Enhancers	HSMMtube	muscle
30	chr11:93257200-93260400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr11:93257200-93264800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:93257400-93259000	Enhancers	Stomach Smooth Muscle	stomach
33	chr11:93257400-93259200	Enhancers	Adipose Nuclei	Adipose
34	chr11:93257400-93259400	Enhancers	Colonic Mucosa	Colon
35	chr11:93257400-93260400	Enhancers	Left Ventricle	heart
36	chr11:93257400-93260600	Enhancers	Fetal Intestine Large	intestine
37	chr11:93257400-93260800	Enhancers	Primary hematopoietic stem cells	blood
38	chr11:93257400-93264000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr11:93257400-93264800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr11:93257400-93266600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr11:93257600-93259200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:93257600-93260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:93257600-93260600	Enhancers	Duodenum Mucosa	Duodenum
44	chr11:93257600-93260600	Enhancers	Fetal Intestine Small	intestine
45	chr11:93257600-93260600	Enhancers	Stomach Mucosa	stomach
46	chr11:93257600-93261000	Enhancers	Placenta	Placenta
47	chr11:93257600-93261000	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr11:93257600-93263000	Enhancers	HepG2	liver
49	chr11:93257600-93264000	Enhancers	Right Ventricle	heart
50	chr11:93257600-93264400	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links