Variant report

Variant	rs393338
Chromosome Location	chr4:48359014-48359015
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	chr4:48351553..48354497-chr4:48357846..48360207,2	MCF-7	breast:
2	chr4:48343973..48346063-chr4:48356828..48359174,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13101954	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13142082	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1352432	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1466631	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1844149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2029347	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291476	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28840724	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34239305	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34380340	0.80[AFR][1000 genomes]
rs35265097	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35963236	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs36157430	0.83[ASN][1000 genomes]
rs366168	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375259	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs384885	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3943122	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs397257	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs401463	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs409911	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4694894	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4695374	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56089943	0.80[AFR][1000 genomes]
rs565234	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs565385	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62309450	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62311260	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6447629	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66671150	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6819696	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6819847	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73246021	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73246023	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48344800-48362400	Weak transcription	Gastric	stomach
2	chr4:48346000-48362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:48346200-48362400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:48346400-48361200	Weak transcription	Thymus	Thymus
5	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr4:48347200-48359600	Weak transcription	Fetal Stomach	stomach
7	chr4:48347400-48362200	Weak transcription	Brain Substantia Nigra	brain
8	chr4:48347400-48362200	Weak transcription	NHLF	lung
9	chr4:48347600-48365000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:48348600-48362400	Weak transcription	Fetal Lung	lung
11	chr4:48348800-48363000	Weak transcription	Hela-S3	cervix
12	chr4:48348800-48371000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:48349400-48361800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:48349400-48361800	Weak transcription	HMEC	breast
15	chr4:48349400-48362200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:48349600-48363200	Weak transcription	Adipose Nuclei	Adipose
17	chr4:48349600-48364400	Weak transcription	Right Atrium	heart
18	chr4:48350000-48375800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr4:48351400-48361400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:48351400-48362600	Weak transcription	A549	lung
21	chr4:48352400-48362200	Weak transcription	Left Ventricle	heart
22	chr4:48352800-48372400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:48353000-48371200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr4:48353200-48362800	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:48353200-48362800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:48353600-48362200	Weak transcription	Brain Anterior Caudate	brain
27	chr4:48353600-48362200	Weak transcription	Fetal Heart	heart
28	chr4:48353600-48363200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr4:48353800-48362400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:48353800-48369200	Weak transcription	Pancreas	Pancrea
31	chr4:48354800-48362200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:48354800-48362400	Weak transcription	Right Ventricle	heart
33	chr4:48355000-48359800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:48355000-48361200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:48355000-48361600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:48355000-48361800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:48355000-48362400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:48355000-48376600	Weak transcription	Primary B cells from cord blood	blood
39	chr4:48355000-48380000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
41	chr4:48355200-48363200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:48355200-48377600	Weak transcription	Fetal Intestine Small	intestine
43	chr4:48355200-48379800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:48355400-48363000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:48355400-48371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:48355800-48390600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr4:48356000-48362800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:48356600-48367800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:48357000-48359200	Enhancers	Muscle Satellite Cultured Cells	--
50	chr4:48357200-48362200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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