Variant report

Variant	rs17440909
Chromosome Location	chr5:58957831-58957832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58803367..58805536-chr5:58956722..58959458,2	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]
rs10043265	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10043283	0.83[CHB][hapmap]
rs10514857	0.83[CHB][hapmap]
rs11949859	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12152908	0.84[EUR][1000 genomes]
rs12187752	0.83[CHB][hapmap]
rs12188131	0.84[ASN][1000 genomes]
rs13155799	0.83[CHB][hapmap]
rs1362941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1362942	0.84[ASN][1000 genomes]
rs1437124	0.83[CHB][hapmap]
rs16877195	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17310599	0.94[CEU][hapmap]
rs17369708	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17381667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17381695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17381723	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17382202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17441217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17441825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17742120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17742544	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17743216	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17799161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2017574	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164660	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3898713	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4699942	0.83[CHB][hapmap]
rs4699943	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4700340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4700341	0.83[CHB][hapmap]
rs55868825	0.84[ASN][1000 genomes]
rs56199003	0.84[ASN][1000 genomes]
rs6450528	0.83[CHB][hapmap]
rs6450530	0.83[CHB][hapmap]
rs6860907	0.83[CHB][hapmap]
rs6889294	0.82[CHB][hapmap]
rs6897073	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs72751211	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72751218	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72751226	0.81[ASN][1000 genomes]
rs72751229	0.84[ASN][1000 genomes]
rs72751231	0.84[ASN][1000 genomes]
rs72751232	0.84[ASN][1000 genomes]
rs72751233	0.84[ASN][1000 genomes]
rs72751234	0.84[ASN][1000 genomes]
rs72751235	0.84[ASN][1000 genomes]
rs72751237	0.84[ASN][1000 genomes]
rs72751241	0.84[ASN][1000 genomes]
rs72751244	0.84[ASN][1000 genomes]
rs72751247	0.84[ASN][1000 genomes]
rs72751250	0.84[ASN][1000 genomes]
rs72751252	0.81[ASN][1000 genomes]
rs756211	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs756212	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7703963	0.82[JPT][hapmap]
rs7708952	0.82[CHB][hapmap]
rs7736817	0.83[CHB][hapmap]
rs877745	0.83[CHB][hapmap]
rs981230	0.83[CHB][hapmap]

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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58948000-58961600	Weak transcription	Gastric	stomach
2	chr5:58954600-58958600	Enhancers	Stomach Mucosa	stomach
3	chr5:58954800-58958000	Enhancers	Primary hematopoietic stem cells	blood
4	chr5:58954800-58958400	Enhancers	Fetal Intestine Small	intestine
5	chr5:58955000-58958000	Enhancers	Primary B cells from cord blood	blood
6	chr5:58956000-58959000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:58956000-58959000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:58956200-58958400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr5:58956400-58958000	Enhancers	HUVEC	blood vessel
10	chr5:58956400-58958400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:58956400-58958400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr5:58956400-58958600	Enhancers	Hela-S3	cervix
13	chr5:58956400-58958600	Enhancers	HSMMtube	muscle
14	chr5:58956600-58958000	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr5:58956600-58958200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr5:58956600-58958200	Enhancers	Brain Cingulate Gyrus	brain
17	chr5:58956600-58958400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr5:58957000-58958000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:58957000-58958200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:58957000-58958200	Enhancers	Small Intestine	intestine
21	chr5:58957200-58958000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr5:58957200-58958000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:58957200-58958000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:58957200-58958000	Enhancers	GM12878-XiMat	blood
25	chr5:58957200-58958200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:58957200-58958200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:58957200-58958200	Enhancers	Psoas Muscle	Psoas
28	chr5:58957200-58958400	Enhancers	Primary B cells from peripheral blood	blood
29	chr5:58957200-58958400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr5:58957200-58958400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr5:58957200-58958400	Enhancers	HepG2	liver
32	chr5:58957200-58958600	Enhancers	Fetal Lung	lung
33	chr5:58957400-58958200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:58957400-58958200	Enhancers	Brain Substantia Nigra	brain
35	chr5:58957400-58958600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:58957400-58959600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:58957400-58960800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:58957600-58958000	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr5:58957600-58958000	Enhancers	Aorta	Aorta
40	chr5:58957600-58958000	Enhancers	Liver	Liver
41	chr5:58957600-58958000	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr5:58957600-58958000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr5:58957600-58958000	Enhancers	Thymus	Thymus
44	chr5:58957600-58958200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr5:58957600-58958200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:58957600-58958200	Enhancers	Fetal Intestine Large	intestine
47	chr5:58957600-58958200	Enhancers	Fetal Thymus	thymus
48	chr5:58957600-58958200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr5:58957600-58958400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr5:58957600-58958400	Enhancers	NH-A	brain

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