Variant report

Variant	rs490212
Chromosome Location	chr7:71743905-71743906
allele	A/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	USF1	chr7:71743530-71743941	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CALN1	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10251307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1232509	0.95[AFR][1000 genomes]
rs1232511	1.00[AFR][1000 genomes]
rs1232518	0.90[AFR][1000 genomes]
rs1914379	1.00[AMR][1000 genomes]
rs2428279	0.84[AFR][1000 genomes]
rs2428281	0.82[AFR][1000 genomes]
rs2521199	1.00[AFR][1000 genomes]
rs2521200	1.00[AFR][1000 genomes]
rs2521202	0.90[AFR][1000 genomes]
rs2521204	0.84[AFR][1000 genomes]
rs2677278	0.95[AFR][1000 genomes]
rs2677280	1.00[AFR][1000 genomes]
rs2677283	0.84[AFR][1000 genomes]
rs2677286	0.84[AFR][1000 genomes]
rs2944836	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2968535	1.00[AMR][1000 genomes]
rs2968536	1.00[AMR][1000 genomes]
rs4295535	0.84[AFR][1000 genomes]
rs4442008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4518555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4601191	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs472164	0.90[AFR][1000 genomes]
rs472884	0.95[AFR][1000 genomes]
rs484279	0.84[AFR][1000 genomes]
rs484343	1.00[AFR][1000 genomes]
rs495774	0.90[AFR][1000 genomes]
rs498441	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs502780	0.90[AFR][1000 genomes]
rs502865	0.90[AFR][1000 genomes]
rs510451	0.84[AFR][1000 genomes]
rs511253	0.84[AFR][1000 genomes]
rs513388	1.00[AFR][1000 genomes]
rs523703	0.95[AFR][1000 genomes]
rs525723	0.90[AFR][1000 genomes]
rs531685	0.84[AFR][1000 genomes]
rs533150	0.90[AFR][1000 genomes]
rs536128	0.84[AFR][1000 genomes]
rs548750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs550322	0.84[AFR][1000 genomes]
rs563410	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs564528	0.84[AFR][1000 genomes]
rs567653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs568003	0.86[AFR][1000 genomes]
rs569837	0.84[AFR][1000 genomes]
rs572043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs573987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs575357	0.84[AFR][1000 genomes]
rs579471	1.00[AFR][1000 genomes]
rs581297	0.95[AFR][1000 genomes]
rs6460705	0.84[AFR][1000 genomes]
rs6460706	0.84[AFR][1000 genomes]
rs6460712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6946262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6948582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6949384	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6968000	1.00[AMR][1000 genomes]
rs6969123	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7791150	0.84[AFR][1000 genomes]
rs844714	0.84[AFR][1000 genomes]
rs859999	0.84[AFR][1000 genomes]
rs860009	0.84[AFR][1000 genomes]
rs864168	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531372	chr7:71300090-71909517	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv491610	chr7:71422560-71803630	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv531373	chr7:71487076-71765613	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv817506	chr7:71488542-71935721	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1034282	chr7:71531113-71876617	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv529620	chr7:71604785-71935721	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv492243	chr7:71648955-71935721	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1019700	chr7:71677836-71844973	Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv538943	chr7:71677836-71844973	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv607460	chr7:71713735-71817899	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1033860	chr7:71715105-71778772	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv538944	chr7:71715105-71778772	Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1032591	chr7:71715105-71794258	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv538945	chr7:71715105-71794258	Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv470299	chr7:71740458-71815170	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv464556	chr7:71740458-71817899	Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71732600-71760600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:71732800-71758000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:71733600-71744000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:71734800-71744200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:71742600-71744600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:71743000-71745000	Genic enhancers	Fetal Thymus	thymus
7	chr7:71743000-71745800	Genic enhancers	Thymus	Thymus
8	chr7:71743200-71744400	Enhancers	Brain Anterior Caudate	brain
9	chr7:71743200-71744800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:71743400-71744600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:71743400-71747400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:71743800-71744400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr7:71743800-71748200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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