Variant report

Variant	rs13245583
Chromosome Location	chr7:56606479-56606480
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	ZNF143	chr7:56606225-56606645	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:56606331-56606531	Raji	blood:	n/a	n/a
3	SIN3A	chr7:56606334-56606692	H1-hESC	embryonic stem cell:	n/a	n/a
4	RCOR1	chr7:56606326-56606523	K562	blood:	n/a	n/a
5	MAZ	chr7:56606396-56606596	K562	blood:	n/a	chr7:56606411-56606421
6	CHD2	chr7:56606369-56606520	HepG2	liver:	n/a	n/a
7	CHD2	chr7:56606395-56606526	GM12878	blood:	n/a	n/a
8	ZNF143	chr7:56606324-56606524	K562	blood:	n/a	n/a
9	MXI1	chr7:56606395-56606530	GM12878	blood:	n/a	n/a
10	STAT1	chr7:56606432-56606527	GM12878	blood:	n/a	n/a
11	MAX	chr7:56606429-56606531	HepG2	liver:	n/a	n/a
12	RCOR1	chr7:56606403-56606529	HepG2	liver:	n/a	n/a
13	CHD2	chr7:56606327-56606527	K562	blood:	n/a	n/a
14	MAX	chr7:56606394-56606529	NB4	blood:	n/a	chr7:56606411-56606421

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88665773..88666293-chr7:56605897..56606515,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233288	TF binding region

Extended variants
information (count: 95 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10215049	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215705	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10226486	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10226756	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10232356	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10235121	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs10236798	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10242086	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs10249023	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10256440	0.95[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10259576	0.90[CEU][hapmap]
rs10266889	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10269082	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10272852	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10281482	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10282398	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105304	0.93[EUR][1000 genomes]
rs1105305	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs1105306	0.93[EUR][1000 genomes]
rs11976165	0.90[CHB][hapmap]
rs11977998	0.91[EUR][1000 genomes]
rs11978242	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12155162	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12155169	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12719002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12719003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227258	0.96[YRI][hapmap]
rs13229926	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13231784	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13307736	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13312340	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1352444	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387067	0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1532083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1601913	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1606628	0.90[CHB][hapmap]
rs1606629	0.82[CHB][hapmap]
rs1849671	0.82[CHB][hapmap]
rs1849672	0.90[CHB][hapmap]
rs1906626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906629	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34135483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34270096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34340801	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34593554	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34765785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35043412	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35483986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749502	0.93[ASN][1000 genomes]
rs3828495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285439	0.93[EUR][1000 genomes]
rs4442091	0.93[EUR][1000 genomes]
rs4947553	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56869388	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66831640	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67173162	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6944931	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6952677	0.93[EUR][1000 genomes]
rs6952857	0.93[EUR][1000 genomes]
rs6955935	0.90[EUR][1000 genomes]
rs6957076	0.90[EUR][1000 genomes]
rs6957105	0.93[EUR][1000 genomes]
rs6968161	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6968398	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7357108	0.95[CEU][hapmap];0.89[YRI][hapmap]
rs7458882	0.91[EUR][1000 genomes]
rs7782035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782889	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7783143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796117	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7799034	0.91[CHB][hapmap]
rs7804839	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656713	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656714	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526294	chr7:56171489-56622630	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1016771	chr7:56174828-56643856	Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv538862	chr7:56174828-56643856	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1033163	chr7:56307057-56677865	ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv538863	chr7:56307057-56677865	ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv427783	chr7:56334626-56983646	Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv1022563	chr7:56383876-57318888	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
8	nsv1016255	chr7:56453095-56835595	ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv888066	chr7:56466740-56693762	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1028678	chr7:56511649-56795206	ZNF genes & repeats Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv538864	chr7:56511649-56795206	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv1020833	chr7:56511848-57323499	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
13	nsv538865	chr7:56511848-57323499	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
14	nsv8090	chr7:56511877-56772523	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv1017561	chr7:56512618-57334136	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
16	esv3432	chr7:56561673-56611316	ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv831009	chr7:56566629-56754313	ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56604800-56607000	ZNF genes & repeats	Pancreas	Pancrea
2	chr7:56604800-56609600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:56605000-56606800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr7:56605000-56611400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:56605200-56606600	Active TSS	Brain Angular Gyrus	brain
6	chr7:56605200-56606600	Active TSS	Brain Substantia Nigra	brain
7	chr7:56605200-56606600	ZNF genes & repeats	Esophagus	oesophagus
8	chr7:56605200-56606600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
9	chr7:56605200-56606800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
10	chr7:56605200-56606800	Active TSS	Stomach Smooth Muscle	stomach
11	chr7:56605200-56607200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
12	chr7:56605200-56612600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
13	chr7:56605400-56606600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
14	chr7:56605400-56606800	ZNF genes & repeats	Adipose Nuclei	Adipose
15	chr7:56605600-56606600	Active TSS	Colon Smooth Muscle	Colon
16	chr7:56605600-56607000	ZNF genes & repeats	Lung	lung
17	chr7:56605600-56608000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:56605600-56610600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:56605800-56606600	Active TSS	Brain Hippocampus Middle	brain
20	chr7:56605800-56606600	ZNF genes & repeats	Spleen	Spleen
21	chr7:56606000-56606600	Active TSS	Brain Anterior Caudate	brain
22	chr7:56606200-56606600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:56606200-56606800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
24	chr7:56606200-56606800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:56606200-56609200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
26	chr7:56606400-56606600	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
27	chr7:56606400-56606600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr7:56606400-56606600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr7:56606400-56606600	Enhancers	Ovary	ovary
30	chr7:56606400-56606600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
31	chr7:56606400-56606800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
32	chr7:56606400-56606800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:56606400-56606800	ZNF genes & repeats	Fetal Muscle Trunk	muscle

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