Variant report

Variant	rs58457441
Chromosome Location	chr3:56650582-56650583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:56650093-56650979	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:56650285-56650614	SK-N-SH	brain:	n/a	n/a
3	MAFK	chr3:56650162-56651062	GM12878	blood:	n/a	chr3:56650692-56650707
4	BACH1	chr3:56650516-56650965	K562	blood:	n/a	n/a
5	MAFK	chr3:56650525-56650954	HepG2	liver:	n/a	chr3:56650692-56650707
6	MAFK	chr3:56650509-56650888	K562	blood:	n/a	chr3:56650692-56650707
7	POLR2A	chr3:56650411-56650809	K562	blood:	n/a	n/a
8	MAFK	chr3:56650514-56650890	HepG2	liver:	n/a	chr3:56650692-56650707
9	MAFK	chr3:56650512-56650947	Hela-S3	cervix:	n/a	chr3:56650692-56650707
10	MAFF	chr3:56650512-56650906	HepG2	liver:	n/a	chr3:56650690-56650708
11	EP300	chr3:56650555-56650720	K562	blood:	n/a	n/a
12	POLR2A	chr3:56648967-56664047	K562	blood:	n/a	n/a
13	BACH1	chr3:56650518-56650959	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAFF	chr3:56650515-56650889	K562	blood:	n/a	chr3:56650690-56650708
15	MAFK	chr3:56650513-56650891	IMR90	lung:	n/a	chr3:56650692-56650707
16	MAFK	chr3:56650523-56650888	H1-hESC	embryonic stem cell:	n/a	chr3:56650692-56650707

Variant related genes	Relation type
CCDC66	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs11130522	0.92[EUR][1000 genomes]
rs1388252	0.92[EUR][1000 genomes]
rs1491162	0.92[EUR][1000 genomes]
rs1491167	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17216678	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17216712	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17216754	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288866	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288873	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306930	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306931	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276465	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276467	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276469	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4292200	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56758331	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57861120	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59835031	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59897254	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60606369	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61456176	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61654248	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61747994	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62249737	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62251182	0.92[EUR][1000 genomes]
rs62251183	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251186	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62251188	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251190	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251192	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62251193	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251197	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251228	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251229	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251230	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251233	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62251235	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251238	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251239	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251240	0.81[EUR][1000 genomes]
rs62251241	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251244	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251245	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254329	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62255965	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62255966	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62255967	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255969	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255970	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255971	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255972	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255973	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255974	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255977	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255978	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255980	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62255981	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256011	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256013	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62256014	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256017	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256018	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256019	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256020	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256022	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62256023	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782254	0.89[EUR][1000 genomes]
rs6788512	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802548	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6810125	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73075746	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081816	0.92[EUR][1000 genomes]
rs73081836	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73081850	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73083715	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083725	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635945	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955247	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
3	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
5	chr3:56640400-56650800	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:56640800-56650600	Weak transcription	HSMMtube	muscle
8	chr3:56640800-56650800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:56644200-56664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:56644400-56652000	Strong transcription	Fetal Lung	lung
14	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:56644600-56655800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:56644600-56665600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:56644800-56655400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:56644800-56656000	Strong transcription	Fetal Muscle Leg	muscle
20	chr3:56644800-56669800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:56645000-56650600	Weak transcription	A549	lung
23	chr3:56645000-56650800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:56645200-56651600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:56645200-56657000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:56645400-56653800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:56645400-56667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr3:56645600-56650600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:56645600-56653400	Weak transcription	Fetal Heart	heart
31	chr3:56645600-56656000	Strong transcription	Fetal Intestine Large	intestine
32	chr3:56645600-56656000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr3:56645600-56664800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:56645600-56665800	Strong transcription	Hela-S3	cervix
35	chr3:56645800-56662000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:56645800-56663800	Strong transcription	HSMM	muscle
37	chr3:56646000-56662800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:56646200-56659200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:56646600-56650600	Weak transcription	Left Ventricle	heart
40	chr3:56646600-56669000	Weak transcription	Small Intestine	intestine
41	chr3:56646800-56658800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:56646800-56659200	Weak transcription	Fetal Intestine Small	intestine
43	chr3:56646800-56673600	Weak transcription	Right Ventricle	heart
44	chr3:56647000-56658400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:56647000-56662000	Weak transcription	Esophagus	oesophagus
46	chr3:56647000-56663000	Strong transcription	Liver	Liver
47	chr3:56647000-56664000	Strong transcription	Adipose Nuclei	Adipose
48	chr3:56647000-56666800	Weak transcription	Lung	lung
49	chr3:56647000-56672200	Weak transcription	Gastric	stomach
50	chr3:56647200-56662600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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