Variant report

Variant	rs3792824
Chromosome Location	chr5:40754221-40754222
allele	C/T
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:40753118..40757884-chr5:40795999..40799979,7	MCF-7	breast:
2	chr5:40752902..40758440-chr5:40826185..40833524,16	K562	blood:
3	chr5:40752864..40755012-chr5:40756548..40758806,2	MCF-7	breast:
4	chr5:40745599..40747692-chr5:40753558..40755440,2	MCF-7	breast:
5	chr5:40753675..40755258-chr5:40838374..40840873,3	K562	blood:
6	chr5:40745635..40751387-chr5:40751429..40754891,8	K562	blood:
7	chr5:40753427..40755619-chr5:40793452..40795341,2	K562	blood:
8	chr5:40752834..40759871-chr5:40793841..40803866,19	K562	blood:
9	chr5:40753276..40755081-chr5:40822441..40825001,2	MCF-7	breast:
10	chr5:40753675..40755359-chr5:40838537..40842271,3	K562	blood:
11	chr5:40753631..40759305-chr5:40833742..40838306,12	K562	blood:
12	chr5:40749464..40751000-chr5:40753765..40756000,2	K562	blood:
13	chr5:40753789..40755953-chr5:40763164..40764930,2	K562	blood:
14	chr5:40753823..40758906-chr5:40833676..40836936,8	MCF-7	breast:
15	chr5:40752681..40758776-chr5:40831589..40836413,12	MCF-7	breast:
16	chr5:40752902..40758869-chr5:40832024..40838409,16	K562	blood:
17	chr5:40753845..40758533-chr5:40769118..40772000,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000132357	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000212296	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10035235	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10053664	0.90[ASN][1000 genomes]
rs12514352	0.93[ASN][1000 genomes]
rs12517210	0.96[ASN][1000 genomes]
rs12518018	0.80[EUR][1000 genomes]
rs12520058	0.96[ASN][1000 genomes]
rs12523329	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792827	0.96[ASN][1000 genomes]
rs3805489	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805490	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805492	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805494	0.95[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805498	0.81[EUR][1000 genomes]
rs3805499	0.90[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs4957350	0.96[ASN][1000 genomes]
rs62357564	0.93[ASN][1000 genomes]
rs7719692	0.96[ASN][1000 genomes]
rs7721093	0.96[ASN][1000 genomes]
rs9800106	0.96[ASN][1000 genomes]

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	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40722800-40755200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:40736000-40755200	Weak transcription	Pancreas	Pancrea
3	chr5:40741800-40754400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:40741800-40754400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:40741800-40754400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:40742000-40754400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:40742000-40754800	Weak transcription	Aorta	Aorta
8	chr5:40742000-40755200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:40742000-40755200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:40742000-40755400	Weak transcription	Spleen	Spleen
11	chr5:40742200-40754600	Weak transcription	Adipose Nuclei	Adipose
12	chr5:40742400-40754800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr5:40742400-40755000	Weak transcription	Placenta	Placenta
14	chr5:40742800-40754400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:40743200-40754600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:40745600-40754400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:40746000-40754400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:40746600-40754800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:40747200-40754400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr5:40747200-40754600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:40747200-40755200	Weak transcription	Small Intestine	intestine
22	chr5:40752200-40754400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:40752400-40754800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr5:40753400-40754600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr5:40753600-40754400	Enhancers	Brain Anterior Caudate	brain
26	chr5:40753600-40754600	Enhancers	HepG2	liver
27	chr5:40753600-40754800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:40753800-40754400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr5:40753800-40754600	Enhancers	Colon Smooth Muscle	Colon
30	chr5:40753800-40754600	Enhancers	Fetal Heart	heart
31	chr5:40754000-40754400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:40754000-40754400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:40754000-40754600	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr5:40754000-40754600	Enhancers	HUVEC	blood vessel
35	chr5:40754000-40754800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr5:40754000-40754800	Enhancers	Liver	Liver
37	chr5:40754000-40755000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr5:40754200-40754400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:40754200-40754400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:40754200-40754400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr5:40754200-40754400	Enhancers	Primary T cells from cord blood	blood
42	chr5:40754200-40754400	Enhancers	Primary hematopoietic stem cells	blood
43	chr5:40754200-40754400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:40754200-40754400	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr5:40754200-40754400	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr5:40754200-40754400	Enhancers	Brain Substantia Nigra	brain
47	chr5:40754200-40754400	Enhancers	Duodenum Mucosa	Duodenum
48	chr5:40754200-40754400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr5:40754200-40754400	Flanking Active TSS	Fetal Brain Male	brain
50	chr5:40754200-40754400	Enhancers	Fetal Kidney	kidney

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