Variant report

Variant	rs55884041
Chromosome Location	chr5:58956437-58956438
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:58801872..58802902-chr5:58956210..58957251,7	MCF-7	breast:
2	chr5:58802090..58802764-chr5:58956093..58957045,3	MCF-7	breast:
3	chr5:58803075..58803840-chr5:58956390..58957074,2	MCF-7	breast:
4	chr5:58821597..58822483-chr5:58956197..58956887,3	MCF-7	breast:
5	chr5:58685998..58686505-chr5:58956311..58957192,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1813481	1.00[AMR][1000 genomes]
rs1813482	1.00[AMR][1000 genomes]
rs1813483	1.00[AMR][1000 genomes]
rs3903515	1.00[AMR][1000 genomes]
rs56012406	1.00[AMR][1000 genomes]
rs56075849	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56125266	1.00[AMR][1000 genomes]
rs56143170	1.00[AMR][1000 genomes]
rs56378519	1.00[AMR][1000 genomes]
rs57438370	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58287048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59281772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60661960	1.00[AMR][1000 genomes]
rs60858267	1.00[AMR][1000 genomes]
rs61332617	1.00[AMR][1000 genomes]
rs61610216	1.00[AMR][1000 genomes]
rs6877740	1.00[AMR][1000 genomes]
rs73758503	1.00[AMR][1000 genomes]
rs73758504	1.00[AMR][1000 genomes]
rs73758505	1.00[AMR][1000 genomes]
rs73758506	1.00[AMR][1000 genomes]
rs73758507	1.00[AMR][1000 genomes]
rs73758509	1.00[AMR][1000 genomes]
rs73758510	1.00[AMR][1000 genomes]
rs73758511	1.00[AMR][1000 genomes]
rs73758512	1.00[AMR][1000 genomes]
rs73758513	1.00[AMR][1000 genomes]
rs73758840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73758841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73758842	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73758854	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73758861	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73758863	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73758866	1.00[AMR][1000 genomes]
rs73758869	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73758874	1.00[AMR][1000 genomes]
rs73758875	1.00[AMR][1000 genomes]
rs73758878	1.00[AMR][1000 genomes]
rs73758879	1.00[AMR][1000 genomes]
rs73758880	1.00[AMR][1000 genomes]
rs73758881	1.00[AMR][1000 genomes]
rs73758884	1.00[AMR][1000 genomes]
rs73758885	1.00[AMR][1000 genomes]
rs73758888	1.00[AMR][1000 genomes]
rs73758889	1.00[AMR][1000 genomes]
rs73758898	1.00[AMR][1000 genomes]
rs73758901	1.00[AMR][1000 genomes]
rs73760361	1.00[AMR][1000 genomes]
rs73760362	1.00[AMR][1000 genomes]
rs73760365	1.00[AMR][1000 genomes]
rs73760616	1.00[AMR][1000 genomes]
rs73760618	1.00[AMR][1000 genomes]
rs73760620	1.00[AMR][1000 genomes]
rs73760622	1.00[AMR][1000 genomes]
rs73761011	1.00[AMR][1000 genomes]
rs73761528	1.00[AMR][1000 genomes]
rs73761530	1.00[AMR][1000 genomes]
rs7723589	1.00[AMR][1000 genomes]
rs931856	1.00[AMR][1000 genomes]
rs931857	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv462190	chr5:58936943-59023870	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv598258	chr5:58936943-59023870	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1034283	chr5:58940594-59040762	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv537767	chr5:58940594-59040762	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58923600-58957200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:58948000-58961600	Weak transcription	Gastric	stomach
3	chr5:58952000-58957600	Weak transcription	Liver	Liver
4	chr5:58952200-58956600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:58952400-58957600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:58954400-58957800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:58954600-58956800	Enhancers	Primary B cells from peripheral blood	blood
8	chr5:58954600-58957800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr5:58954600-58958600	Enhancers	Stomach Mucosa	stomach
10	chr5:58954800-58956600	Enhancers	Fetal Intestine Large	intestine
11	chr5:58954800-58957800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:58954800-58958000	Enhancers	Primary hematopoietic stem cells	blood
13	chr5:58954800-58958400	Enhancers	Fetal Intestine Small	intestine
14	chr5:58955000-58957400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:58955000-58958000	Enhancers	Primary B cells from cord blood	blood
16	chr5:58955400-58956600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:58955400-58957200	Weak transcription	Fetal Lung	lung
18	chr5:58955400-58957800	Enhancers	Colon Smooth Muscle	Colon
19	chr5:58955600-58957200	Enhancers	A549	lung
20	chr5:58955800-58956600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:58955800-58957800	Enhancers	Rectal Smooth Muscle	rectum
22	chr5:58956000-58957000	Weak transcription	Small Intestine	intestine
23	chr5:58956000-58957200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:58956000-58957200	Weak transcription	Psoas Muscle	Psoas
25	chr5:58956000-58957200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:58956000-58957600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:58956000-58957600	Weak transcription	Aorta	Aorta
28	chr5:58956000-58959000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:58956000-58959000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:58956200-58958400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr5:58956400-58956600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:58956400-58956600	Enhancers	Brain Hippocampus Middle	brain
33	chr5:58956400-58956600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:58956400-58956600	Enhancers	GM12878-XiMat	blood
35	chr5:58956400-58956600	Enhancers	HSMM	muscle
36	chr5:58956400-58957000	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr5:58956400-58957000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:58956400-58957400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr5:58956400-58957800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr5:58956400-58957800	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr5:58956400-58958000	Enhancers	HUVEC	blood vessel
42	chr5:58956400-58958400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:58956400-58958400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr5:58956400-58958600	Enhancers	Hela-S3	cervix
45	chr5:58956400-58958600	Enhancers	HSMMtube	muscle

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