Variant report

Variant	rs11740439
Chromosome Location	chr5:127295353-127295354
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:127294744..127297859-chr5:127418074..127420896,5	MCF-7	breast:
2	chr5:127292969..127298749-chr5:127417448..127421101,7	MCF-7	breast:
3	chr5:127263364..127266213-chr5:127293562..127295793,3	MCF-7	breast:
4	chr5:127293751..127296384-chr5:127304334..127306609,2	MCF-7	breast:
5	chr5:127291358..127294527-chr5:127295144..127299558,4	K562	blood:
6	chr5:127211016..127213453-chr5:127292897..127295874,2	MCF-7	breast:
7	chr5:127293327..127295485-chr5:127298267..127301058,2	MCF-7	breast:
8	chr5:127293170..127295868-chr5:127299899..127303794,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000245937	Chromatin interaction
ENSG00000064651	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10037914	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10065448	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10072806	0.85[GIH][hapmap];0.83[JPT][hapmap]
rs10074995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10079317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10463834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10478787	0.84[JPT][hapmap]
rs10900794	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11740438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11741283	0.94[ASN][1000 genomes]
rs12517005	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12523625	0.84[JPT][hapmap]
rs12653621	0.86[ASN][1000 genomes]
rs12658023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1520246	1.00[JPT][hapmap]
rs2286386	0.80[ASN][1000 genomes]
rs2409037	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28473744	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28542972	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28567046	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28591675	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28636438	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28687461	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28736542	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28816429	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4836345	1.00[JPT][hapmap]
rs55896045	0.94[ASN][1000 genomes]
rs6877403	0.94[ASN][1000 genomes]
rs6892704	0.84[JPT][hapmap]
rs6898956	0.94[ASN][1000 genomes]
rs732236	0.84[JPT][hapmap]
rs9327457	1.00[JPT][hapmap]
rs9327458	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127274800-127296000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:127278400-127295600	Weak transcription	HSMMtube	muscle
3	chr5:127281800-127295400	Weak transcription	Psoas Muscle	Psoas
4	chr5:127285800-127303800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:127287400-127297200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr5:127290600-127332000	Weak transcription	Aorta	Aorta
7	chr5:127290800-127295400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:127290800-127297400	Weak transcription	Spleen	Spleen
9	chr5:127292200-127297600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:127292400-127296400	Enhancers	Left Ventricle	heart
11	chr5:127292600-127296400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr5:127292600-127296400	Enhancers	HepG2	liver
13	chr5:127292600-127298400	Enhancers	Fetal Intestine Large	intestine
14	chr5:127292600-127298600	Enhancers	Fetal Intestine Small	intestine
15	chr5:127292800-127295600	Enhancers	Brain Anterior Caudate	brain
16	chr5:127292800-127296200	Enhancers	Brain Substantia Nigra	brain
17	chr5:127292800-127296400	Enhancers	Brain Hippocampus Middle	brain
18	chr5:127292800-127297200	Enhancers	Fetal Lung	lung
19	chr5:127292800-127297600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr5:127292800-127297800	Enhancers	HUVEC	blood vessel
21	chr5:127292800-127298400	Enhancers	Fetal Heart	heart
22	chr5:127292800-127314400	Weak transcription	Pancreas	Pancrea
23	chr5:127293000-127295600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:127293000-127295800	Flanking Active TSS	A549	lung
25	chr5:127293000-127297600	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr5:127293000-127298600	Enhancers	Stomach Mucosa	stomach
27	chr5:127293200-127295400	Weak transcription	HSMM	muscle
28	chr5:127293200-127297400	Weak transcription	Gastric	stomach
29	chr5:127293200-127301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:127293200-127301800	Weak transcription	Ovary	ovary
31	chr5:127293200-127303600	Weak transcription	Esophagus	oesophagus
32	chr5:127293400-127295400	Weak transcription	NHDF-Ad	bronchial
33	chr5:127293400-127296200	Weak transcription	Right Ventricle	heart
34	chr5:127293400-127297200	Weak transcription	Right Atrium	heart
35	chr5:127293600-127295400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr5:127293600-127295400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr5:127293600-127295800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:127293600-127301800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:127293800-127296200	Enhancers	Brain Angular Gyrus	brain
40	chr5:127294000-127295400	Weak transcription	Colonic Mucosa	Colon
41	chr5:127294000-127295600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:127294000-127295600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr5:127294000-127296400	Enhancers	Fetal Thymus	thymus
44	chr5:127294200-127297200	Enhancers	Dnd41	blood
45	chr5:127294200-127297600	Enhancers	Adipose Nuclei	Adipose
46	chr5:127294200-127297600	Enhancers	Rectal Smooth Muscle	rectum
47	chr5:127294400-127296000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:127294400-127296200	Enhancers	Fetal Stomach	stomach
49	chr5:127294400-127296400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:127294400-127302800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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