Variant report

Variant	rs6483249
Chromosome Location	chr11:93249941-93249942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93246116..93247653-chr11:93249759..93251907,2	K562	blood:

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

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

rs_ID	r²[population]
rs11020372	1.00[AFR][1000 genomes]
rs11020387	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11020388	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11020390	0.98[EUR][1000 genomes]
rs11603107	0.88[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	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11604399	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606253	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606261	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606262	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	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790221	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12791489	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12795164	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12796609	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12806700	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12808921	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305660	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305661	0.97[AMR][1000 genomes];0.97[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	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35901746	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35930354	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3793999	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794002	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794007	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794008	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58462328	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483248	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7111773	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7130465	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71480681	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71480682	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71480685	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7928401	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7933953	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945684	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897558	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
rs6483249	SMCO4	cis	Whole Blood	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93211000-93253400	Weak transcription	Primary T cells from cord blood	blood
2	chr11:93218600-93254400	Weak transcription	Hela-S3	cervix
3	chr11:93226400-93257400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:93227200-93257600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:93233000-93257400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr11:93234800-93250400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:93235200-93250200	Weak transcription	Aorta	Aorta
8	chr11:93235400-93257800	Weak transcription	Gastric	stomach
9	chr11:93235600-93258800	Weak transcription	Small Intestine	intestine
10	chr11:93235800-93252600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr11:93238400-93259000	Weak transcription	Fetal Lung	lung
12	chr11:93239600-93255600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:93241000-93252400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr11:93241000-93254200	Weak transcription	HepG2	liver
15	chr11:93241800-93257400	Weak transcription	Fetal Intestine Large	intestine
16	chr11:93243200-93252200	Weak transcription	Dnd41	blood
17	chr11:93243400-93250000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:93243800-93255600	Weak transcription	Fetal Intestine Small	intestine
19	chr11:93244000-93254400	Weak transcription	Pancreas	Pancrea
20	chr11:93244200-93253800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:93244800-93254000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:93246400-93250200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr11:93248000-93261800	Weak transcription	Fetal Stomach	stomach
24	chr11:93248800-93250600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:93248800-93250800	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr11:93248800-93251000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr11:93248800-93257400	Weak transcription	Adipose Nuclei	Adipose
28	chr11:93249000-93250000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:93249000-93250600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:93249000-93250600	Weak transcription	NHEK	skin
31	chr11:93249000-93252400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:93249000-93252600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr11:93249000-93261600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:93249200-93250200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:93249200-93250200	Weak transcription	GM12878-XiMat	blood
36	chr11:93249200-93250400	Weak transcription	Fetal Thymus	thymus
37	chr11:93249200-93250800	Weak transcription	Liver	Liver
38	chr11:93249200-93251800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:93249200-93252200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:93249200-93252200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr11:93249200-93253600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:93249200-93253600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:93249200-93254400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:93249200-93254400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr11:93249200-93255400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:93249200-93255600	Weak transcription	Left Ventricle	heart
47	chr11:93249200-93255600	Weak transcription	Right Ventricle	heart
48	chr11:93249200-93257600	Weak transcription	Fetal Muscle Leg	muscle
49	chr11:93249200-93257600	Weak transcription	Placenta	Placenta
50	chr11:93249200-93257800	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links