Variant report

Variant	rs4680453
Chromosome Location	chr3:158377797-158377798
allele	C/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	GATA2	chr3:158377342-158377906	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr3:158377523-158377811	Gliobla	brain:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
3	FOS	chr3:158377533-158377936	HUVEC	blood vessel:	n/a	n/a
4	UBTF	chr3:158377685-158377815	K562	blood:	n/a	n/a
5	RAD21	chr3:158377530-158377826	H1-hESC	embryonic stem cell:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
6	POLR2A	chr3:158377087-158377850	PANC-1	pancreas:	n/a	n/a
7	MAX	chr3:158377551-158377878	NB4	blood:	n/a	n/a
8	FOS	chr3:158377573-158377855	MCF10A-Er-Src	breast:	n/a	n/a
9	RAD21	chr3:158377265-158377916	SK-N-SH	brain:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
10	CTCF	chr3:158377528-158377805	MCF-7	breast:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
11	POLR2A	chr3:158377448-158378153	HUVEC	blood vessel:	n/a	n/a
12	CTCF	chr3:158377438-158377810	K562	blood:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
13	SMC3	chr3:158377491-158377845	K562	blood:	n/a	chr3:158377661-158377671 chr3:158377657-158377671
14	RAD21	chr3:158377492-158377865	Hela-S3	cervix:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
15	RAD21	chr3:158377519-158377826	H1-hESC	embryonic stem cell:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
16	RAD21	chr3:158377568-158377814	HepG2	liver:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
17	CTCF	chr3:158377516-158377856	A549	lung:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
18	CTCF	chr3:158377259-158378041	A549	lung:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
19	CTCF	chr3:158377297-158378062	SK-N-SH	brain:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
20	CTCF	chr3:158377442-158377882	K562	blood:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
21	TCF12	chr3:158377346-158377925	A549	lung:	n/a	n/a
22	SMC3	chr3:158377265-158377943	SK-N-SH	brain:	n/a	chr3:158377661-158377671 chr3:158377657-158377671
23	SIN3AK20	chr3:158377495-158377925	A549	lung:	n/a	n/a
24	RAD21	chr3:158377488-158377875	ECC-1	luminal epithelium:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
25	RAD21	chr3:158377422-158377915	A549	lung:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
26	USF2	chr3:158377641-158377841	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr3:158377404-158377944	MCF-7	breast:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
28	CTCF	chr3:158377493-158377837	Spleen_OC	spleen:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
29	RAD21	chr3:158377378-158377938	MCF-7	breast:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
30	JUN	chr3:158377562-158378122	HUVEC	blood vessel:	n/a	n/a
31	RAD21	chr3:158377430-158377895	HCT-116	colon:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
32	MXI1	chr3:158377235-158378100	IMR90	lung:	n/a	n/a
33	GATA3	chr3:158377203-158377813	T-47D	breast:	n/a	chr3:158377205-158377212 chr3:158377203-158377212 chr3:158377203-158377213 chr3:158377205-158377212 chr3:158377205-158377212
34	MAFF	chr3:158377513-158377881	K562	blood:	n/a	n/a
35	RAD21	chr3:158377537-158377834	HepG2	liver:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
36	HCFC1	chr3:158377557-158377800	K562	blood:	n/a	n/a
37	RAD21	chr3:158377387-158377904	A549	lung:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
38	CTCF	chr3:158377516-158377800	GM12878	blood:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
39	CTCF	chr3:158377518-158377850	H1-hESC	embryonic stem cell:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
40	BACH1	chr3:158377589-158377823	K562	blood:	n/a	n/a
41	CTCF	chr3:158377466-158377823	K562	blood:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
42	JUND	chr3:158377500-158377835	K562	blood:	n/a	n/a
43	SMC3	chr3:158377481-158377882	Hela-S3	cervix:	n/a	chr3:158377661-158377671 chr3:158377657-158377671
44	CTCF	chr3:158377392-158377895	IMR90	lung:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
45	MAFK	chr3:158377516-158377939	K562	blood:	n/a	n/a
46	CTCF	chr3:158377513-158377797	HepG2	liver:	n/a	chr3:158377655-158377673 chr3:158377658-158377671
47	MXI1	chr3:158377612-158377814	K562	blood:	n/a	n/a
48	ZNF143	chr3:158377532-158377887	K562	blood:	n/a	n/a
49	RAD21	chr3:158377439-158377881	SK-N-SH_RA	brain:	n/a	chr3:158377659-158377672 chr3:158377661-158377671 chr3:158377656-158377675
50	CTCF	chr3:158377492-158377827	A549	lung:	n/a	chr3:158377655-158377673 chr3:158377658-158377671

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158377338..158378185-chr3:158390076..158390932,2	MCF-7	breast:

Variant related genes	Relation type
GFM1	TF binding region
ENSG00000079257	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1038886	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1047366	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1075551	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10936158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12107643	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12496174	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12639052	0.97[EUR][1000 genomes]
rs13074694	0.91[ASN][1000 genomes]
rs13324770	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13325932	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1369563	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1435642	0.90[ASN][1000 genomes]
rs1602760	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1620229	0.88[ASN][1000 genomes]
rs1656377	0.81[ASN][1000 genomes]
rs1714516	0.88[ASN][1000 genomes]
rs17629360	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17629390	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17629414	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1836688	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1864503	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864507	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2115943	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2248924	0.91[ASN][1000 genomes]
rs2276773	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303909	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364274	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2566344	0.90[ASN][1000 genomes]
rs2573179	0.90[ASN][1000 genomes]
rs2731112	0.88[ASN][1000 genomes]
rs2731118	0.90[ASN][1000 genomes]
rs2731120	0.86[ASN][1000 genomes]
rs2731122	0.90[ASN][1000 genomes]
rs28481597	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2933550	0.88[ASN][1000 genomes]
rs3765025	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3845272	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851361	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851363	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680445	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680449	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680450	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680451	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680452	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680457	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4875	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62287933	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441212	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6441220	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6763812	0.84[ASN][1000 genomes]
rs6771248	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6772483	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6777711	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6781342	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6800914	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6802317	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6803047	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6803608	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6804259	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7609717	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7613814	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7621897	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7631310	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7653826	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891464	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819567	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9819631	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9824985	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9844502	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9848908	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9864508	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3399089	chr3:158356055-158410094	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4680453	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs4680453	MLF1	cis	Esophagus Mucosa	GTEx
rs4680453	MLF1	cis	Heart Left Ventricle	GTEx
rs4680453	LXN	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158362800-158389600	Weak transcription	Gastric	stomach
2	chr3:158362800-158389800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:158362800-158390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:158363000-158378200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:158363000-158379800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:158363000-158381800	Weak transcription	Esophagus	oesophagus
7	chr3:158363200-158378600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:158363200-158389400	Weak transcription	Fetal Brain Male	brain
9	chr3:158363600-158379000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:158363600-158389400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:158363800-158388200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:158363800-158388600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:158364000-158385400	Weak transcription	Fetal Heart	heart
14	chr3:158364000-158387400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:158364000-158388400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr3:158364200-158378600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:158364200-158379000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:158364200-158385800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:158364200-158388200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:158364400-158377800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:158364400-158388600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:158364800-158380400	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:158364800-158388000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr3:158364800-158391000	Strong transcription	Dnd41	blood
25	chr3:158365800-158378800	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:158365800-158379600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:158366400-158388000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:158366800-158378800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:158367000-158387600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:158368000-158378800	Weak transcription	Psoas Muscle	Psoas
31	chr3:158368400-158378200	Weak transcription	Thymus	Thymus
32	chr3:158368400-158378400	Weak transcription	Brain Anterior Caudate	brain
33	chr3:158368400-158378800	Weak transcription	Right Ventricle	heart
34	chr3:158369600-158388200	Strong transcription	Placenta	Placenta
35	chr3:158369800-158388200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:158370000-158385000	Strong transcription	Hela-S3	cervix
37	chr3:158370600-158378600	Weak transcription	Lung	lung
38	chr3:158370600-158379000	Weak transcription	Aorta	Aorta
39	chr3:158370600-158386200	Weak transcription	Small Intestine	intestine
40	chr3:158370800-158378400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:158370800-158378800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:158371200-158377800	Weak transcription	HepG2	liver
43	chr3:158371200-158378600	Weak transcription	NH-A	brain
44	chr3:158371600-158378600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:158372200-158389800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:158373000-158378400	Weak transcription	NHEK	skin
47	chr3:158373000-158378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:158373000-158380000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:158373000-158384200	Weak transcription	Colonic Mucosa	Colon
50	chr3:158374000-158378000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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