Variant report

Variant	rs11939903
Chromosome Location	chr4:88256137-88256138
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11097131	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs11734330	0.82[YRI][hapmap]
rs11930147	0.82[AFR][1000 genomes]
rs11930151	0.82[AFR][1000 genomes]
rs11931674	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11934060	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11939415	0.82[AFR][1000 genomes]
rs11940002	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11946391	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11946465	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12505484	0.82[AFR][1000 genomes]
rs55663915	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55878019	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55879514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55933669	1.00[AMR][1000 genomes]
rs55968517	1.00[AMR][1000 genomes]
rs55974821	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56113853	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56196275	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56293231	1.00[AMR][1000 genomes]
rs56336118	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56788263	0.82[AFR][1000 genomes]
rs57088507	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57743836	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57806008	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57948983	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58637341	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58985971	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59037460	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59137232	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59157345	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59311794	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59476561	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59593300	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60371489	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60404847	0.85[AMR][1000 genomes]
rs60661283	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60690297	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60955120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61262236	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61367052	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61514672	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61594871	1.00[AMR][1000 genomes]
rs61646372	1.00[AFR][1000 genomes]
rs62305729	0.80[AFR][1000 genomes]
rs62305730	0.82[AFR][1000 genomes]
rs62305731	0.82[AFR][1000 genomes]
rs62305732	0.82[AFR][1000 genomes]
rs6820688	1.00[AMR][1000 genomes]
rs73839181	0.85[AMR][1000 genomes]
rs73839185	1.00[AMR][1000 genomes]
rs73839189	1.00[AMR][1000 genomes]
rs73839191	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839192	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841125	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841126	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841128	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73841136	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841139	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841140	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841141	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841142	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841143	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841144	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841145	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7660178	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7665638	0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7671726	0.85[AMR][1000 genomes]
rs7698406	0.80[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv4412	chr4:88237813-88283368	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88250600-88259400	Weak transcription	Fetal Heart	heart
2	chr4:88253400-88256200	ZNF genes & repeats	Primary B cells from cord blood	blood
3	chr4:88253600-88256200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:88253800-88256600	ZNF genes & repeats	Dnd41	blood
5	chr4:88253800-88258000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr4:88253800-88274600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:88254000-88256200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr4:88254000-88256200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:88254000-88256200	ZNF genes & repeats	Liver	Liver
10	chr4:88254200-88256400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:88254400-88256400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
12	chr4:88254800-88257800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:88254800-88258800	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:88254800-88258800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:88254800-88260200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:88254800-88266000	Weak transcription	Brain Angular Gyrus	brain
17	chr4:88254800-88266000	Weak transcription	Fetal Kidney	kidney
18	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:88255000-88257200	Weak transcription	Small Intestine	intestine
20	chr4:88255000-88260200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:88255000-88260600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:88255000-88263000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:88255000-88263200	Weak transcription	HSMM	muscle
24	chr4:88255000-88266000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:88255000-88268200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr4:88255000-88292400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:88255200-88256600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
28	chr4:88255200-88256800	Weak transcription	Fetal Intestine Small	intestine
29	chr4:88255200-88257200	Weak transcription	Left Ventricle	heart
30	chr4:88255200-88257600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
31	chr4:88255200-88267800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr4:88255200-88274400	Weak transcription	GM12878-XiMat	blood
33	chr4:88255200-88285600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr4:88255200-88293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:88255400-88259600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:88255400-88261000	Strong transcription	Fetal Lung	lung
37	chr4:88255400-88263200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr4:88255400-88264600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr4:88255600-88256800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
40	chr4:88255600-88256800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
41	chr4:88255600-88257600	Weak transcription	Adipose Nuclei	Adipose
42	chr4:88255600-88266200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:88255800-88256800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
44	chr4:88255800-88257600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr4:88255800-88259200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr4:88255800-88266200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:88255800-88278200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:88256000-88256800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr4:88256000-88257200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:88256000-88257200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links