Variant report

Variant	rs12658940
Chromosome Location	chr5:56989529-56989530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:56978767..56981076-chr5:56987149..56990064,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10057804	1.00[ASN][1000 genomes]
rs10077188	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs10487615	1.00[ASN][1000 genomes]
rs12153068	1.00[EUR][1000 genomes]
rs12189365	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12652479	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12654040	1.00[ASN][1000 genomes]
rs12654351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654850	0.83[EUR][1000 genomes]
rs12654963	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12655658	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16887298	1.00[ASN][1000 genomes]
rs2215419	0.98[ASN][1000 genomes]
rs4700209	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58041565	0.91[ASN][1000 genomes]
rs58245968	0.95[EUR][1000 genomes]
rs58266257	1.00[ASN][1000 genomes]
rs59516621	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59697426	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60219417	0.89[EUR][1000 genomes]
rs61220614	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6862527	0.91[ASN][1000 genomes]
rs6876911	0.89[EUR][1000 genomes]
rs6883451	0.95[EUR][1000 genomes]
rs6883485	0.95[EUR][1000 genomes]
rs73085594	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089817	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089845	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73089868	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73089872	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73089877	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73089897	0.83[EUR][1000 genomes]
rs7702309	1.00[CEU][hapmap]
rs7713500	1.00[CEU][hapmap]
rs7714714	1.00[ASN][1000 genomes]
rs7717808	1.00[ASN][1000 genomes]
rs7729312	1.00[CEU][hapmap]
rs7731160	1.00[CEU][hapmap]
rs7734079	1.00[ASN][1000 genomes]
rs7734787	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:56985600-56990400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:56986600-56989800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:56986800-56991800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:56987000-56992800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:56987200-56989800	Enhancers	K562	blood
6	chr5:56987400-56994800	Weak transcription	Right Ventricle	heart
7	chr5:56987600-56991400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:56987600-56991800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:56988200-56989600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:56988200-56989600	Enhancers	Ovary	ovary
11	chr5:56988200-56990000	Enhancers	Brain Cingulate Gyrus	brain
12	chr5:56988200-56993400	Enhancers	Brain Angular Gyrus	brain
13	chr5:56988400-56989600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:56988400-56989600	Enhancers	Psoas Muscle	Psoas
15	chr5:56988400-56989600	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr5:56988400-56989600	Enhancers	NHLF	lung
17	chr5:56988400-56989800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr5:56988400-56989800	Enhancers	HSMMtube	muscle
19	chr5:56988400-56989800	Enhancers	NHDF-Ad	bronchial
20	chr5:56988400-56990000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:56988400-56990000	Enhancers	Fetal Intestine Small	intestine
22	chr5:56988400-56990000	Enhancers	Hela-S3	cervix
23	chr5:56988400-56990000	Enhancers	HUVEC	blood vessel
24	chr5:56988400-56990200	Flanking Active TSS	A549	lung
25	chr5:56988400-56990200	Enhancers	NH-A	brain
26	chr5:56988400-56990600	Enhancers	HepG2	liver
27	chr5:56988400-56991600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:56988400-56991800	Enhancers	Fetal Lung	lung
29	chr5:56988600-56989600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr5:56988600-56989600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:56988600-56989600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr5:56988600-56989600	Enhancers	Fetal Intestine Large	intestine
33	chr5:56988600-56989800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr5:56988600-56989800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr5:56988600-56989800	Enhancers	Brain Substantia Nigra	brain
36	chr5:56988600-56995400	Enhancers	Adipose Nuclei	Adipose
37	chr5:56988800-56989600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr5:56988800-56989600	Enhancers	Stomach Mucosa	stomach
39	chr5:56988800-56989800	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr5:56988800-56989800	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr5:56989000-56989600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr5:56989000-56989800	Enhancers	H9 Cell Line	embryonic stem cell
43	chr5:56989000-56990200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:56989000-56990200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:56989000-56992000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr5:56989200-56989600	Flanking Active TSS	HMEC	breast
47	chr5:56989200-56989600	Flanking Active TSS	HSMM	muscle
48	chr5:56989200-56989600	Flanking Active TSS	NHEK	skin
49	chr5:56989200-56989800	Enhancers	H1 Cell Line	embryonic stem cell
50	chr5:56989200-56989800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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