Variant report

Variant	rs4864583
Chromosome Location	chr4:57276196-57276197
allele	C/T
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	STAT3	chr4:57276104-57276886	MCF10A-Er-Src	breast:	n/a	chr4:57276647-57276654
2	GABPA	chr4:57276152-57277216	MCF-7	breast:	n/a	n/a
3	IRF1	chr4:57276113-57276276	K562	blood:	n/a	n/a
4	FOS	chr4:57276195-57276903	HUVEC	blood vessel:	n/a	n/a
5	NFIC	chr4:57276001-57276961	SK-N-SH	brain:	n/a	n/a
6	MXI1	chr4:57274987-57277307	SK-N-SH	brain:	n/a	chr4:57276622-57276637 chr4:57276620-57276635
7	REST	chr4:57276183-57277154	H1-neurons	neurons:	n/a	n/a
8	FOS	chr4:57276174-57276853	MCF10A-Er-Src	breast:	n/a	n/a
9	FOXM1	chr4:57276089-57276916	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr4:57276189-57277010	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57275040..57277242-chr4:57300118..57301937,2	MCF-7	breast:
2	chr4:57274956..57277925-chr4:57332751..57335099,2	MCF-7	breast:
3	chr4:57275711..57277429-chr4:57298915..57301727,2	K562	blood:

Variant related genes	Relation type
PPAT	TF binding region
ENSG00000268171	TF binding region
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000174780	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10008223	0.93[ASN][1000 genomes]
rs10013402	0.95[ASN][1000 genomes]
rs10017460	0.94[ASN][1000 genomes]
rs10051	0.81[ASN][1000 genomes]
rs10434444	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs10434445	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10461357	0.83[ASN][1000 genomes]
rs1060472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11133442	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1124569	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12498340	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12501334	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501502	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12503412	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504291	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12505939	0.81[ASN][1000 genomes]
rs12508008	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12509542	0.83[ASN][1000 genomes]
rs12510712	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12511770	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12513091	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12646890	0.83[ASN][1000 genomes]
rs13147900	0.91[JPT][hapmap]
rs1401904	0.90[JPT][hapmap]
rs1401906	0.90[JPT][hapmap]
rs14211	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1474179	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1520026	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1520030	1.00[CEU][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17086696	0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.95[ASN][1000 genomes]
rs17086794	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17086832	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs17086853	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1967559	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1983378	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2030366	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2271923	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28510634	0.93[ASN][1000 genomes]
rs28866881	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796541	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3822001	0.81[CEU][hapmap]
rs4263445	0.86[ASN][1000 genomes]
rs4340842	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4346704	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4493603	1.00[CEU][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4618376	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4864579	0.92[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4864580	0.95[ASN][1000 genomes]
rs4865088	0.86[ASN][1000 genomes]
rs4865089	0.87[ASN][1000 genomes]
rs4865092	0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4865103	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4865107	0.83[ASN][1000 genomes]
rs4865108	0.81[ASN][1000 genomes]
rs5010012	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55915354	0.81[ASN][1000 genomes]
rs56040009	0.81[ASN][1000 genomes]
rs56099714	0.83[ASN][1000 genomes]
rs56392224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56887793	0.97[ASN][1000 genomes]
rs58151706	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61032900	0.86[ASN][1000 genomes]
rs6554345	0.91[JPT][hapmap]
rs6554358	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs66810706	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66858948	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs66863699	0.83[ASN][1000 genomes]
rs67957495	0.86[ASN][1000 genomes]
rs6820279	0.86[ASN][1000 genomes]
rs6820314	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821301	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6824893	0.80[ASN][1000 genomes]
rs6829250	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832797	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6834696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6834736	0.90[JPT][hapmap]
rs6846895	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6849183	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6855041	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs7664841	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7670991	0.91[ASN][1000 genomes]
rs7696808	0.84[YRI][hapmap]
rs8340	1.00[CHB][hapmap];0.90[YRI][hapmap];0.89[ASN][1000 genomes]
rs9799864	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4864583	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs4864583	SRP72	cis	Adipose Subcutaneous	GTEx
rs4864583	SRP72	cis	Esophagus Mucosa	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
2	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
5	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
6	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:57255200-57276400	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:57255200-57276600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:57255200-57276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:57255200-57276600	Weak transcription	Brain Substantia Nigra	brain
11	chr4:57255400-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:57255800-57276600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:57256000-57276400	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:57256200-57276600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:57256400-57276600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
17	chr4:57264400-57276400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:57267600-57276200	Weak transcription	HSMM	muscle
21	chr4:57267600-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:57267800-57277600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:57267800-57278400	Weak transcription	Placenta	Placenta
24	chr4:57270200-57276800	Weak transcription	Colonic Mucosa	Colon
25	chr4:57272000-57276200	Weak transcription	Fetal Intestine Large	intestine
26	chr4:57272000-57276400	Weak transcription	HSMMtube	muscle
27	chr4:57272200-57276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:57272200-57276400	Weak transcription	Aorta	Aorta
29	chr4:57272200-57276400	Weak transcription	Ovary	ovary
30	chr4:57272200-57276600	Weak transcription	Fetal Intestine Small	intestine
31	chr4:57272400-57276600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:57272600-57276200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:57272600-57276400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr4:57272600-57276400	Weak transcription	Adipose Nuclei	Adipose
35	chr4:57272600-57276600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:57272600-57280200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:57272800-57276200	Weak transcription	Liver	Liver
38	chr4:57272800-57276200	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:57272800-57276600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr4:57272800-57276600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:57272800-57276600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr4:57272800-57280400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr4:57272800-57281600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr4:57272800-57292600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
46	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
47	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:57273000-57276400	Weak transcription	HepG2	liver
49	chr4:57273000-57276800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:57273200-57276800	Weak transcription	Hela-S3	cervix

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