Variant report

Variant	rs7716309
Chromosome Location	chr5:111524545-111524546
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	CTCF	chr5:111524400-111524550	GM12864	blood:	n/a	n/a
2	POLR2A	chr5:111524312-111524668	K562	blood:	n/a	n/a
3	CTCF	chr5:111524520-111524670	HPAF	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:111496468..111499243-chr5:111522477..111524816,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251187	TF binding region
ENSG00000238363	Chromatin interaction
ENSG00000224032	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10037824	1.00[ASN][1000 genomes]
rs10040749	1.00[ASN][1000 genomes]
rs10043186	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10054560	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10054610	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10056561	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10065740	1.00[ASN][1000 genomes]
rs10068493	1.00[ASN][1000 genomes]
rs10069011	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070995	1.00[ASN][1000 genomes]
rs1020951	1.00[ASN][1000 genomes]
rs10463433	1.00[ASN][1000 genomes]
rs10477478	1.00[ASN][1000 genomes]
rs10478073	1.00[ASN][1000 genomes]
rs1054724	1.00[ASN][1000 genomes]
rs1078128	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241153	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241160	1.00[ASN][1000 genomes]
rs12186685	1.00[ASN][1000 genomes]
rs12187589	1.00[ASN][1000 genomes]
rs12188700	1.00[ASN][1000 genomes]
rs12189034	1.00[ASN][1000 genomes]
rs12655385	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13153601	1.00[ASN][1000 genomes]
rs13165611	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1366144	1.00[ASN][1000 genomes]
rs1427978	1.00[ASN][1000 genomes]
rs1560052	1.00[ASN][1000 genomes]
rs1560053	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560054	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560055	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560057	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560058	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560061	1.00[ASN][1000 genomes]
rs17134319	1.00[ASN][1000 genomes]
rs17134348	1.00[ASN][1000 genomes]
rs17271934	1.00[ASN][1000 genomes]
rs17343994	1.00[ASN][1000 genomes]
rs1863960	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1896620	1.00[ASN][1000 genomes]
rs1896621	1.00[ASN][1000 genomes]
rs1975015	1.00[ASN][1000 genomes]
rs1981954	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2114991	1.00[ASN][1000 genomes]
rs2416277	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27413	1.00[ASN][1000 genomes]
rs4602685	1.00[ASN][1000 genomes]
rs4957632	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957634	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957636	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958002	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958003	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958004	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958007	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4958008	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4958009	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958010	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958012	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958013	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958014	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958015	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958020	1.00[ASN][1000 genomes]
rs4958025	1.00[ASN][1000 genomes]
rs55639430	1.00[ASN][1000 genomes]
rs55796748	1.00[ASN][1000 genomes]
rs55829200	1.00[ASN][1000 genomes]
rs55845736	1.00[ASN][1000 genomes]
rs55913426	1.00[ASN][1000 genomes]
rs56108405	1.00[ASN][1000 genomes]
rs56288086	1.00[ASN][1000 genomes]
rs56293447	1.00[ASN][1000 genomes]
rs56307310	1.00[ASN][1000 genomes]
rs56881711	1.00[ASN][1000 genomes]
rs57428532	1.00[ASN][1000 genomes]
rs59537089	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60636568	1.00[ASN][1000 genomes]
rs61061658	1.00[ASN][1000 genomes]
rs62367266	1.00[ASN][1000 genomes]
rs62372421	1.00[ASN][1000 genomes]
rs6594566	1.00[ASN][1000 genomes]
rs6594567	1.00[ASN][1000 genomes]
rs6594569	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594571	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594574	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594577	1.00[ASN][1000 genomes]
rs6594588	1.00[ASN][1000 genomes]
rs66521031	1.00[ASN][1000 genomes]
rs66892745	1.00[ASN][1000 genomes]
rs67033649	1.00[ASN][1000 genomes]
rs67586008	1.00[ASN][1000 genomes]
rs67631852	1.00[ASN][1000 genomes]
rs6863063	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872947	1.00[ASN][1000 genomes]
rs6876893	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878423	1.00[ASN][1000 genomes]
rs6884589	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893877	1.00[ASN][1000 genomes]
rs6894036	1.00[ASN][1000 genomes]
rs72781655	1.00[ASN][1000 genomes]
rs72781664	1.00[ASN][1000 genomes]
rs72781668	1.00[ASN][1000 genomes]
rs72781677	1.00[ASN][1000 genomes]
rs72781678	1.00[ASN][1000 genomes]
rs7703522	1.00[ASN][1000 genomes]
rs7704087	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706160	1.00[CEU][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709484	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710973	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711158	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717160	1.00[ASN][1000 genomes]
rs7717363	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719346	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722291	1.00[ASN][1000 genomes]
rs821736	1.00[ASN][1000 genomes]
rs821749	1.00[ASN][1000 genomes]
rs890757	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890758	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh 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	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111497600-111538600	Weak transcription	Small Intestine	intestine
2	chr5:111501400-111546400	Weak transcription	Spleen	Spleen
3	chr5:111502400-111546400	Weak transcription	Aorta	Aorta
4	chr5:111502800-111546000	Weak transcription	Ovary	ovary
5	chr5:111503600-111527800	Weak transcription	Psoas Muscle	Psoas
6	chr5:111503600-111537400	Weak transcription	Lung	lung
7	chr5:111504800-111541400	Weak transcription	Right Ventricle	heart
8	chr5:111504800-111557800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:111504800-111586400	Weak transcription	Gastric	stomach
10	chr5:111505000-111537400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:111505600-111541800	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:111510800-111540000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:111510800-111547400	Weak transcription	HUVEC	blood vessel
14	chr5:111519000-111546400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:111519200-111532600	Weak transcription	Fetal Kidney	kidney
16	chr5:111519200-111537400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:111519200-111553800	Weak transcription	Pancreas	Pancrea
18	chr5:111519400-111524800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:111519400-111529200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:111519400-111530600	Weak transcription	Left Ventricle	heart
21	chr5:111519400-111531800	Weak transcription	Fetal Heart	heart
22	chr5:111519600-111530400	Weak transcription	Adipose Nuclei	Adipose
23	chr5:111519800-111553600	Weak transcription	Esophagus	oesophagus
24	chr5:111520400-111529400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:111520600-111527800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:111523400-111540600	Weak transcription	Hela-S3	cervix
27	chr5:111523800-111537400	Weak transcription	Rectal Mucosa Donor 29	rectum

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