Variant report

Variant	rs55641278
Chromosome Location	chr3:101290577-101290578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:101290531-101290598	MCF10A-Er-Src	breast:	n/a	n/a
2	FOSL2	chr3:101290349-101290626	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:101290193-101290588	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:101290106-101290592	K562	blood:	n/a	n/a
5	FOS	chr3:101290389-101290688	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr3:101290502-101290622	MCF10A-Er-Src	breast:	n/a	n/a
7	JUND	chr3:101290350-101290694	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:101230224..101236227-chr3:101287209..101294479,8	K562	blood:
2	chr3:101289369..101294999-chr3:101391357..101396813,8	K562	blood:
3	chr3:101289588..101293101-chr3:101394155..101396875,5	MCF-7	breast:
4	chr3:101230038..101233245-chr3:101289410..101293829,6	MCF-7	breast:
5	chr3:101231111..101234614-chr3:101289997..101293015,3	MCF-7	breast:
6	chr3:101212560..101214999-chr3:101290197..101292554,2	K562	blood:
7	chr3:101273703..101276448-chr3:101288119..101291518,3	K562	blood:
8	chr3:101288583..101290158-chr3:101290409..101292112,2	K562	blood:

No data

Variant related genes	Relation type
PCNP	TF binding region
ENSG00000138468	Chromatin interaction
ENSG00000256628	Chromatin interaction
ENSG00000066422	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10936707	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11708616	0.87[EUR][1000 genomes]
rs11708845	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11711808	0.88[EUR][1000 genomes]
rs11715368	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11720560	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12638137	0.81[EUR][1000 genomes]
rs12638796	0.85[EUR][1000 genomes]
rs17345528	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17345786	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17508319	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3762729	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3804775	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3804778	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55710435	0.85[EUR][1000 genomes]
rs57880921	0.85[EUR][1000 genomes]
rs58835747	0.88[EUR][1000 genomes]
rs58907984	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59359251	0.81[EUR][1000 genomes]
rs60837174	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6791964	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72944107	0.85[EUR][1000 genomes]
rs72946021	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73863360	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7641261	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997739	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55641278	SENP7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101281400-101292600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:101281800-101292000	Weak transcription	Colonic Mucosa	Colon
3	chr3:101281800-101292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:101281800-101292200	Weak transcription	Esophagus	oesophagus
5	chr3:101281800-101292200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:101282000-101291800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:101282000-101291800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:101282000-101292200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:101282000-101292200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:101282000-101292200	Weak transcription	Right Atrium	heart
11	chr3:101282200-101291600	Weak transcription	Fetal Lung	lung
12	chr3:101282200-101292200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:101282200-101292600	Weak transcription	Aorta	Aorta
14	chr3:101282400-101291800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:101282400-101292000	Weak transcription	Right Ventricle	heart
16	chr3:101282400-101292200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:101282400-101292400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:101282400-101292600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:101282400-101292600	Weak transcription	Spleen	Spleen
20	chr3:101282600-101292000	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:101282600-101292200	Weak transcription	Small Intestine	intestine
22	chr3:101282800-101291400	Weak transcription	Fetal Heart	heart
23	chr3:101283000-101292600	Weak transcription	Gastric	stomach
24	chr3:101285000-101291600	Weak transcription	Fetal Kidney	kidney
25	chr3:101285000-101291800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:101285000-101291800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:101285000-101292400	Weak transcription	Ovary	ovary
28	chr3:101285200-101291800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:101285200-101292000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:101285200-101292000	Weak transcription	Fetal Brain Male	brain
31	chr3:101285400-101291600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:101285400-101291600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:101285400-101292000	Weak transcription	Brain Angular Gyrus	brain
34	chr3:101285400-101292000	Weak transcription	Brain Anterior Caudate	brain
35	chr3:101285400-101292000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:101285600-101291600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:101285600-101291800	Weak transcription	HSMMtube	muscle
38	chr3:101285600-101292000	Weak transcription	Liver	Liver
39	chr3:101285600-101292000	Weak transcription	Osteobl	bone
40	chr3:101285600-101292200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:101285600-101292200	Weak transcription	Placenta	Placenta
42	chr3:101285600-101292200	Weak transcription	Left Ventricle	heart
43	chr3:101285600-101292600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:101285800-101291800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:101285800-101292000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:101285800-101292000	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:101285800-101292000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:101286000-101291800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:101286000-101292200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:101286200-101292000	Weak transcription	Fetal Intestine Small	intestine

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