Variant report

Variant	rs10003396
Chromosome Location	chr4:53586480-53586481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10000311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs10001085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10001387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs10002261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10010306	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10012676	1.00[ASN][1000 genomes]
rs10014740	1.00[CEU][hapmap]
rs10014752	0.87[ASN][1000 genomes]
rs10014850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs10021143	0.81[ASN][1000 genomes]
rs10023867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs10027906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10029145	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10031386	0.87[ASN][1000 genomes]
rs10032700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs10033218	0.87[ASN][1000 genomes]
rs10471216	0.87[ASN][1000 genomes]
rs13434726	1.00[ASN][1000 genomes]
rs13435157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs28380682	0.81[ASN][1000 genomes]
rs28396506	0.87[ASN][1000 genomes]
rs28402205	0.87[ASN][1000 genomes]
rs28411005	0.87[ASN][1000 genomes]
rs28412170	0.81[ASN][1000 genomes]
rs28430452	0.87[ASN][1000 genomes]
rs28451750	0.81[ASN][1000 genomes]
rs28475600	0.81[ASN][1000 genomes]
rs28478374	0.87[ASN][1000 genomes]
rs28482298	0.81[ASN][1000 genomes]
rs28503210	0.81[ASN][1000 genomes]
rs28565016	0.81[ASN][1000 genomes]
rs28588481	0.81[ASN][1000 genomes]
rs28590396	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28619184	0.81[ASN][1000 genomes]
rs28644292	0.81[ASN][1000 genomes]
rs28654693	0.87[ASN][1000 genomes]
rs28660550	0.87[ASN][1000 genomes]
rs28660571	0.87[ASN][1000 genomes]
rs28672279	0.81[ASN][1000 genomes]
rs28721897	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28722174	0.81[ASN][1000 genomes]
rs28784684	0.87[ASN][1000 genomes]
rs28825412	0.87[ASN][1000 genomes]
rs28849759	0.87[ASN][1000 genomes]
rs28852068	0.87[ASN][1000 genomes]
rs6830833	0.87[ASN][1000 genomes]
rs73815970	0.85[AFR][1000 genomes]
rs9990686	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9994643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9997863	0.83[AFR][1000 genomes];0.87[ASN][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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats 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
4	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1005869	chr4:53571901-53649247	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53580000-53587800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:53580000-53588000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr4:53580000-53588000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:53580000-53588000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:53580200-53587800	Weak transcription	Brain Substantia Nigra	brain
6	chr4:53580200-53587800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:53580200-53588000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:53580200-53588000	Weak transcription	Thymus	Thymus
9	chr4:53580200-53588000	Weak transcription	HSMMtube	muscle
10	chr4:53580400-53587800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:53580400-53587800	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:53580600-53588000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:53581000-53588000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:53581000-53588000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:53581000-53588000	Weak transcription	Aorta	Aorta
16	chr4:53581000-53588000	Weak transcription	Hela-S3	cervix
17	chr4:53581200-53588000	Weak transcription	Colonic Mucosa	Colon
18	chr4:53581400-53587800	Weak transcription	Brain Angular Gyrus	brain
19	chr4:53581600-53587000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:53581600-53587600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:53581600-53587800	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:53581600-53587800	Weak transcription	Stomach Mucosa	stomach
23	chr4:53581600-53587800	Weak transcription	Dnd41	blood
24	chr4:53581600-53588000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:53581600-53588000	Weak transcription	Fetal Kidney	kidney
26	chr4:53581600-53588000	Weak transcription	Pancreas	Pancrea
27	chr4:53581800-53587400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:53581800-53587800	Weak transcription	Small Intestine	intestine
29	chr4:53582000-53587400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:53582000-53588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:53582000-53588000	Weak transcription	Fetal Brain Male	brain
32	chr4:53582000-53588000	Weak transcription	Gastric	stomach
33	chr4:53582000-53588000	Weak transcription	Psoas Muscle	Psoas
34	chr4:53582000-53588000	Weak transcription	Right Ventricle	heart
35	chr4:53582200-53587800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr4:53582200-53587800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr4:53582600-53587800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:53582600-53587800	Weak transcription	A549	lung
39	chr4:53582600-53588000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr4:53582800-53587800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:53582800-53587800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr4:53582800-53587800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:53582800-53587800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:53582800-53587800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:53582800-53587800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:53582800-53587800	Weak transcription	Liver	Liver
47	chr4:53582800-53587800	Weak transcription	Brain Anterior Caudate	brain
48	chr4:53582800-53587800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr4:53582800-53587800	Weak transcription	HSMM	muscle
50	chr4:53582800-53588000	Weak transcription	Spleen	Spleen

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