Variant report

Variant	rs11959397
Chromosome Location	chr5:14349603-14349604
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10866506	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10866507	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11133785	0.85[EUR][1000 genomes]
rs11949756	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11950000	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12109453	0.89[EUR][1000 genomes]
rs12109756	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12109880	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12110161	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12110267	1.00[EUR][1000 genomes]
rs16903421	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903423	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903428	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903434	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16903453	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[EUR][1000 genomes]
rs16903460	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs16903464	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs16903497	0.88[MEX][hapmap]
rs2463803	0.82[CEU][hapmap]
rs35373258	0.89[EUR][1000 genomes]
rs56689214	0.89[EUR][1000 genomes]
rs57017859	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57640930	0.89[EUR][1000 genomes]
rs59405120	0.91[EUR][1000 genomes]
rs60738268	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60768136	0.85[EUR][1000 genomes]
rs60892841	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61059406	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61469842	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62344976	0.85[EUR][1000 genomes]
rs62344979	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62344981	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62344983	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62344984	0.88[EUR][1000 genomes]
rs62345009	0.95[EUR][1000 genomes]
rs62345012	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62345015	0.89[EUR][1000 genomes]
rs66554336	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6883134	0.88[MEX][hapmap]
rs697559	0.82[CEU][hapmap]
rs730185	0.88[EUR][1000 genomes]
rs73061636	0.89[EUR][1000 genomes]
rs7706484	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7710935	0.85[EUR][1000 genomes]
rs7715916	0.89[EUR][1000 genomes]
rs7731443	0.85[EUR][1000 genomes]
rs773764	0.82[CEU][hapmap]
rs773765	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3342821	chr5:14346652-14351350	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14331400-14350000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:14335000-14360600	Weak transcription	Psoas Muscle	Psoas
3	chr5:14338000-14357200	Weak transcription	Colonic Mucosa	Colon
4	chr5:14338400-14358000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:14338800-14357600	Weak transcription	Esophagus	oesophagus
6	chr5:14339200-14357600	Weak transcription	Gastric	stomach
7	chr5:14339200-14358000	Weak transcription	Thymus	Thymus
8	chr5:14339200-14358200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:14339400-14358400	Weak transcription	Fetal Thymus	thymus
10	chr5:14340400-14353800	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr5:14340800-14353600	Strong transcription	HSMM	muscle
12	chr5:14341200-14350400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:14341400-14355000	Weak transcription	Ovary	ovary
14	chr5:14341400-14359400	Weak transcription	Primary T cells from cord blood	blood
15	chr5:14341600-14357400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:14342600-14357200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:14342600-14358200	Weak transcription	Pancreas	Pancrea
18	chr5:14342800-14350000	Weak transcription	Brain Germinal Matrix	brain
19	chr5:14342800-14351000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:14342800-14351600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:14342800-14352000	Strong transcription	Osteobl	bone
22	chr5:14342800-14352200	Strong transcription	NH-A	brain
23	chr5:14342800-14354000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:14342800-14355000	Weak transcription	Right Ventricle	heart
25	chr5:14342800-14357200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:14342800-14357200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:14342800-14365200	Weak transcription	Small Intestine	intestine
28	chr5:14343000-14351200	Strong transcription	Fetal Intestine Large	intestine
29	chr5:14343200-14351600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:14343200-14358800	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:14343400-14352400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:14343400-14357000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:14343600-14350600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:14343600-14350600	Weak transcription	Lung	lung
35	chr5:14343600-14351200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:14343600-14351200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr5:14343600-14357000	Weak transcription	Brain Angular Gyrus	brain
38	chr5:14343600-14357600	Weak transcription	Brain Anterior Caudate	brain
39	chr5:14343800-14350600	Strong transcription	Primary B cells from cord blood	blood
40	chr5:14343800-14362400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:14344000-14351000	Weak transcription	GM12878-XiMat	blood
42	chr5:14344400-14350400	Strong transcription	Adipose Nuclei	Adipose
43	chr5:14344400-14358000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:14344600-14350600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr5:14345000-14355000	Weak transcription	Left Ventricle	heart
46	chr5:14345400-14353800	Weak transcription	Hela-S3	cervix
47	chr5:14345600-14351400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr5:14346000-14351800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr5:14346200-14350000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr5:14346200-14352000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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