Variant report

Variant	rs7933953
Chromosome Location	chr11:93256172-93256173
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11020387	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11020388	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11020390	0.99[EUR][1000 genomes]
rs11603107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11603540	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11603560	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11604399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606505	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11607585	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12789912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790221	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12791489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12795164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12796609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12806700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12808921	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16919026	0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs2305660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305661	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638787	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34028949	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34580908	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34819559	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35364744	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35368196	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35423935	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35901746	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35930354	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3793999	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]
rs3794002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58462328	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6483249	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111773	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7130465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71480681	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71480682	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71480685	0.89[EUR][1000 genomes]
rs7365	1.00[CHB][hapmap]
rs7928401	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7945684	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897555	1.00[CEU][hapmap]
rs897558	1.00[CHB][hapmap];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
rs7933953	SMCO4	cis	Whole Blood	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93226400-93257400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr11:93227200-93257600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:93233000-93257400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:93235400-93257800	Weak transcription	Gastric	stomach
5	chr11:93235600-93258800	Weak transcription	Small Intestine	intestine
6	chr11:93238400-93259000	Weak transcription	Fetal Lung	lung
7	chr11:93241800-93257400	Weak transcription	Fetal Intestine Large	intestine
8	chr11:93248000-93261800	Weak transcription	Fetal Stomach	stomach
9	chr11:93248800-93257400	Weak transcription	Adipose Nuclei	Adipose
10	chr11:93249000-93261600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:93249200-93257600	Weak transcription	Fetal Muscle Leg	muscle
12	chr11:93249200-93257600	Weak transcription	Placenta	Placenta
13	chr11:93249200-93257800	Weak transcription	Right Atrium	heart
14	chr11:93251000-93258200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:93251000-93261400	Weak transcription	Fetal Brain Male	brain
16	chr11:93251000-93261600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:93251000-93261600	Weak transcription	Aorta	Aorta
18	chr11:93252000-93257000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:93252000-93266800	Enhancers	Fetal Thymus	thymus
20	chr11:93252200-93257000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr11:93252200-93259000	Enhancers	Liver	Liver
22	chr11:93252200-93260800	Enhancers	Dnd41	blood
23	chr11:93252400-93257000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:93252600-93259800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr11:93253000-93257200	Weak transcription	HSMMtube	muscle
26	chr11:93253000-93258800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:93253200-93256400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr11:93253400-93257600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:93253400-93257600	Weak transcription	Stomach Mucosa	stomach
30	chr11:93253600-93256800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:93253800-93266200	Weak transcription	Fetal Brain Female	brain
32	chr11:93254200-93257000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr11:93254400-93256200	Enhancers	Pancreas	Pancrea
34	chr11:93254400-93256600	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr11:93254600-93256200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr11:93254600-93256400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:93254800-93256200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr11:93254800-93256800	Weak transcription	Osteobl	bone
39	chr11:93254800-93258000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr11:93254800-93258200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr11:93255000-93256200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr11:93255000-93257000	Weak transcription	Thymus	Thymus
43	chr11:93255000-93257400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr11:93255000-93258200	Weak transcription	Primary T cells from cord blood	blood
45	chr11:93255000-93259200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:93255000-93263600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr11:93255000-93274600	Weak transcription	Hela-S3	cervix
48	chr11:93255200-93257200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:93255200-93257800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr11:93255400-93256400	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links