Variant report

Variant	rs59749917
Chromosome Location	chr5:154131585-154131586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:154131382-154131708	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:154130887-154131697	K562	blood:	n/a	n/a
3	IRF1	chr5:154131511-154131649	K562	blood:	n/a	n/a
4	FOS	chr5:154131558-154131708	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:154059219..154066449-chr5:154131053..154139153,28	MCF-7	breast:
2	chr5:154072065..154073573-chr5:154131263..154133221,2	MCF-7	breast:
3	chr5:154062284..154064360-chr5:154130861..154133550,2	MCF-7	breast:
4	chr5:154131390..154134045-chr5:154222442..154224295,2	MCF-7	breast:
5	chr5:154080813..154083048-chr5:154129473..154132225,2	MCF-7	breast:
6	chr5:154121264..154124038-chr5:154128528..154131681,3	MCF-7	breast:

No data

Variant related genes	Relation type
LARP1	TF binding region
ENSG00000221552	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1035368	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12188828	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12300	0.86[EUR][1000 genomes]
rs17116411	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17116414	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17116421	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17116442	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17116534	0.87[EUR][1000 genomes]
rs180846	0.83[EUR][1000 genomes]
rs1974776	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1974777	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2042168	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2112223	0.84[EUR][1000 genomes]
rs2161128	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2258437	0.84[EUR][1000 genomes]
rs2396999	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2431184	0.81[ASN][1000 genomes]
rs2544866	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2544874	0.87[EUR][1000 genomes]
rs2544875	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544876	0.87[EUR][1000 genomes]
rs2544880	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544884	0.83[EUR][1000 genomes]
rs2560063	0.86[EUR][1000 genomes]
rs2644743	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2644744	0.84[EUR][1000 genomes]
rs2644746	0.83[EUR][1000 genomes]
rs2688186	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2688187	0.87[EUR][1000 genomes]
rs2688188	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2688189	0.87[EUR][1000 genomes]
rs2688190	0.87[EUR][1000 genomes]
rs2688191	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2688193	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2688195	0.81[EUR][1000 genomes]
rs2688198	0.87[EUR][1000 genomes]
rs2688199	0.85[EUR][1000 genomes]
rs2688200	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2688201	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2688206	0.87[EUR][1000 genomes]
rs2688208	0.86[EUR][1000 genomes]
rs348739	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs348748	0.83[EUR][1000 genomes]
rs348749	0.84[EUR][1000 genomes]
rs348750	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs348751	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs348752	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs348754	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs39614	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4354100	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs454161	0.81[ASN][1000 genomes]
rs4958771	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55770418	0.83[EUR][1000 genomes]
rs56374414	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58415346	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59525998	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6879277	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6884416	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs702742	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73276742	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73280705	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7723269	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7728194	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs816717	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816718	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816720	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs816722	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816743	0.84[EUR][1000 genomes]
rs9942412	0.88[AMR][1000 genomes];0.91[EUR][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	nsv1021153	chr5:154099869-154147970	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154107200-154133200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr5:154116200-154132400	Weak transcription	Fetal Intestine Small	intestine
3	chr5:154117800-154133000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:154118000-154133000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:154119600-154133400	Weak transcription	Lung	lung
6	chr5:154121000-154132800	Weak transcription	Psoas Muscle	Psoas
7	chr5:154121200-154132600	Weak transcription	Gastric	stomach
8	chr5:154121200-154132800	Weak transcription	Brain Angular Gyrus	brain
9	chr5:154121600-154132600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:154122600-154133000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:154124000-154132800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:154124000-154133000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:154126400-154133200	Weak transcription	Brain Anterior Caudate	brain
14	chr5:154127600-154132600	Weak transcription	Pancreas	Pancrea
15	chr5:154127800-154132600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:154128000-154132600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr5:154128800-154132400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:154128800-154132800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr5:154128800-154133000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:154128800-154133200	Weak transcription	Placenta	Placenta
21	chr5:154128800-154133200	Weak transcription	A549	lung
22	chr5:154129000-154132400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:154129000-154132600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:154129000-154132600	Weak transcription	Fetal Heart	heart
25	chr5:154129000-154132800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr5:154129000-154133000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:154129000-154133200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:154129000-154133400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr5:154129200-154132600	Weak transcription	Left Ventricle	heart
30	chr5:154129200-154133200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr5:154129200-154133400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:154129200-154134000	Weak transcription	Aorta	Aorta
33	chr5:154129400-154132800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:154129600-154132600	Weak transcription	K562	blood
35	chr5:154129600-154132800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr5:154129600-154132800	Weak transcription	Fetal Lung	lung
37	chr5:154130000-154132400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:154130000-154132600	Weak transcription	Fetal Muscle Leg	muscle
39	chr5:154130000-154133000	Weak transcription	Brain Substantia Nigra	brain
40	chr5:154130000-154133000	Weak transcription	Right Atrium	heart
41	chr5:154130800-154132800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:154130800-154132800	Weak transcription	Adipose Nuclei	Adipose
43	chr5:154131000-154132800	Weak transcription	Liver	Liver

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