Variant report

Variant	rs73102285
Chromosome Location	chr5:52155642-52155643
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	RCOR1	chr5:52155308-52156126	IMR90	lung:	n/a	n/a
2	RAD21	chr5:52155474-52155874	SK-N-SH_RA	brain:	n/a	n/a
3	TCF12	chr5:52155236-52156001	SK-N-SH	brain:	n/a	n/a
4	NFIC	chr5:52155287-52156024	SK-N-SH	brain:	n/a	n/a
5	PBX3	chr5:52155441-52156033	SK-N-SH	brain:	n/a	n/a
6	FOS	chr5:52155423-52155801	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr5:52155402-52155733	MCF10A-Er-Src	breast:	n/a	chr5:52155560-52155571
8	FOS	chr5:52155424-52155836	MCF10A-Er-Src	breast:	n/a	n/a
9	TCF12	chr5:52155241-52156113	SK-N-SH	brain:	n/a	n/a
10	JUND	chr5:52155242-52156001	SK-N-SH	brain:	n/a	n/a
11	JUND	chr5:52155274-52156067	SK-N-SH	brain:	n/a	n/a
12	PBX3	chr5:52155388-52155994	SK-N-SH	brain:	n/a	n/a
13	RXRA	chr5:52155434-52155953	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr5:52155245-52156162	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr5:52155538-52155870	IMR90	lung:	n/a	n/a
16	TAF1	chr5:52155447-52155676	SK-N-SH	brain:	n/a	n/a
17	EP300	chr5:52154595-52156190	SK-N-SH	brain:	n/a	n/a
18	TEAD4	chr5:52155251-52155973	SK-N-SH	brain:	n/a	n/a
19	CEBPB	chr5:52155475-52155802	IMR90	lung:	n/a	n/a
20	MAX	chr5:52155332-52155900	SK-N-SH	brain:	n/a	n/a
21	EP300	chr5:52155428-52155898	SK-N-SH_RA	brain:	n/a	n/a
22	TEAD4	chr5:52155311-52155993	SK-N-SH	brain:	n/a	n/a
23	GATA3	chr5:52155305-52156022	SK-N-SH	brain:	n/a	n/a
24	FOSL2	chr5:52155408-52155841	SK-N-SH	brain:	n/a	n/a
25	FOSL2	chr5:52155299-52156001	SK-N-SH	brain:	n/a	n/a
26	STAT3	chr5:52155236-52155680	MCF10A-Er-Src	breast:	n/a	chr5:52155560-52155571
27	JUND	chr5:52155273-52155987	SK-N-SH	brain:	n/a	n/a
28	RAD21	chr5:52155435-52155859	IMR90	lung:	n/a	n/a
29	STAT3	chr5:52155410-52155769	MCF10A-Er-Src	breast:	n/a	chr5:52155560-52155571
30	MAFK	chr5:52155560-52155915	IMR90	lung:	n/a	n/a
31	STAT3	chr5:52155398-52155739	MCF10A-Er-Src	breast:	n/a	chr5:52155560-52155571
32	MYC	chr5:52155497-52155709	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr5:52155461-52155733	MCF10A-Er-Src	breast:	n/a	n/a
34	RAD21	chr5:52155422-52155818	SK-N-SH_RA	brain:	n/a	n/a
35	POLR2A	chr5:52155545-52155716	MCF10A-Er-Src	breast:	n/a	n/a
36	EP300	chr5:52155327-52156081	SK-N-SH	brain:	n/a	n/a
37	MEF2A	chr5:52155372-52155964	SK-N-SH	brain:	n/a	n/a
38	EP300	chr5:52155470-52155932	SK-N-SH_RA	brain:	n/a	n/a
39	FOS	chr5:52155461-52155767	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr5:52155365-52155946	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ITGA1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10038615	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10046016	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513000	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10513001	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949835	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11952083	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11956627	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12110170	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478445	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16880353	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59192299	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60422098	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860395	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880226	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884370	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6886404	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894627	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895807	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896699	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73754051	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73754052	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73754053	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73754054	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73754055	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73754057	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73756267	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73756268	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73756272	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704305	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv830295	chr5:52084532-52257696	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1032554	chr5:52126688-52174119	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52136200-52161400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr5:52142000-52220200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:52142200-52166400	Weak transcription	Spleen	Spleen
4	chr5:52143600-52173600	Weak transcription	Left Ventricle	heart
5	chr5:52143800-52159600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:52145200-52157200	Weak transcription	Fetal Intestine Large	intestine
7	chr5:52145800-52181000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:52146800-52166000	Weak transcription	HepG2	liver
9	chr5:52150000-52156000	Enhancers	NHDF-Ad	bronchial
10	chr5:52150000-52157400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:52150000-52157400	Weak transcription	Aorta	Aorta
12	chr5:52150200-52159000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:52150200-52166400	Weak transcription	Fetal Intestine Small	intestine
14	chr5:52150400-52159200	Weak transcription	Small Intestine	intestine
15	chr5:52150400-52159400	Weak transcription	Fetal Stomach	stomach
16	chr5:52150400-52159600	Weak transcription	Fetal Brain Male	brain
17	chr5:52150600-52157200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:52151400-52158800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:52152600-52157200	Weak transcription	Colon Smooth Muscle	Colon
20	chr5:52153200-52157200	Weak transcription	Liver	Liver
21	chr5:52153200-52163400	Weak transcription	Dnd41	blood
22	chr5:52153200-52166400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:52153600-52159000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:52153600-52159600	Weak transcription	Adipose Nuclei	Adipose
25	chr5:52154000-52164200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:52154200-52166400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:52154800-52156000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:52155000-52156000	Enhancers	HSMMtube	muscle
29	chr5:52155200-52156000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:52155200-52156000	Enhancers	HSMM	muscle
31	chr5:52155200-52156000	Enhancers	NH-A	brain
32	chr5:52155200-52156000	Enhancers	Osteobl	bone
33	chr5:52155200-52156200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr5:52155400-52155800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:52155400-52155800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:52155400-52155800	Enhancers	Fetal Kidney	kidney
37	chr5:52155400-52156000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:52155400-52156000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:52155400-52156800	Enhancers	NHLF	lung
40	chr5:52155600-52155800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:52155600-52155800	Enhancers	HMEC	breast
42	chr5:52155600-52156000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:52155600-52156000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr5:52155600-52156200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:52155600-52156200	Enhancers	Fetal Lung	lung

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