Variant report

Variant	rs1496593
Chromosome Location	chr4:79479683-79479684
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	chr4:79463825..79467444-chr4:79478158..79482300,4	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10213249	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650752	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1390738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496589	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496590	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496592	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1603462	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975147	0.94[ASW][hapmap];0.95[CHD][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6533780	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672582	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7691521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696371	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1496593	CCNI	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79473400-79481400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:79473400-79481400	Weak transcription	HSMM	muscle
3	chr4:79473400-79481600	Weak transcription	Gastric	stomach
4	chr4:79473400-79481600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:79473400-79485400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:79473600-79479800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:79473600-79481400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:79473600-79481600	Weak transcription	Pancreas	Pancrea
9	chr4:79473600-79481800	Weak transcription	Small Intestine	intestine
10	chr4:79473600-79487200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:79473800-79481400	Weak transcription	Aorta	Aorta
12	chr4:79474000-79482200	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:79474400-79481400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:79474400-79481400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:79474400-79481800	Weak transcription	Esophagus	oesophagus
16	chr4:79474400-79486600	Weak transcription	Psoas Muscle	Psoas
17	chr4:79474400-79527200	Weak transcription	Spleen	Spleen
18	chr4:79474600-79480800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:79474600-79481400	Weak transcription	Fetal Stomach	stomach
20	chr4:79474600-79481800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:79474600-79482400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:79474600-79488200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:79474800-79481600	Weak transcription	K562	blood
24	chr4:79475000-79480800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:79475000-79481400	Weak transcription	Fetal Heart	heart
26	chr4:79475000-79481600	Weak transcription	Placenta	Placenta
27	chr4:79475200-79479800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:79475200-79481600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:79475200-79481600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:79475200-79481600	Weak transcription	Lung	lung
31	chr4:79475400-79480000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:79475400-79480800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:79475400-79481200	Weak transcription	NH-A	brain
34	chr4:79475400-79481600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:79475600-79481400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:79475600-79481400	Weak transcription	HSMMtube	muscle
37	chr4:79475600-79482200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:79475600-79483800	Genic enhancers	HMEC	breast
39	chr4:79476800-79486600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:79477000-79480000	Enhancers	A549	lung
41	chr4:79477200-79483000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr4:79477600-79479800	Enhancers	Stomach Mucosa	stomach
43	chr4:79478200-79479800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:79478200-79481000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:79478400-79483600	Enhancers	HUVEC	blood vessel
46	chr4:79478600-79480800	Enhancers	Hela-S3	cervix
47	chr4:79478800-79480200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:79478800-79480200	Weak transcription	Fetal Intestine Small	intestine
49	chr4:79478800-79480200	Weak transcription	Left Ventricle	heart
50	chr4:79478800-79481400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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