Variant report

Variant	rs10000897
Chromosome Location	chr4:96756802-96756803
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	RAD21	chr4:96756772-96757266	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr4:96756714-96757360	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr4:96756731-96757285	HCT-116	colon:	n/a	n/a
4	JUN	chr4:96756801-96756804	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr4:96756763-96757161	MCF-7	breast:	n/a	n/a
6	RAD21	chr4:96756725-96757279	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr4:96756784-96757181	MCF-7	breast:	n/a	n/a
8	CTCF	chr4:96756771-96757273	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:96756581..96757503-chr4:96956588..96957342,2	MCF-7	breast:

Variant related genes	Relation type
PDHA2	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10008305	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10011321	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10019264	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10026739	0.89[ASN][1000 genomes]
rs1006643	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212672	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212751	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10212823	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1076860	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097486	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506801	0.94[ASN][1000 genomes]
rs12510298	0.91[ASN][1000 genomes]
rs13104815	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106992	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107501	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114782	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115178	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1369982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436535	0.94[ASN][1000 genomes]
rs1436539	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436540	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436552	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1816556	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1821736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1836898	0.94[ASN][1000 genomes]
rs1836899	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2219277	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4699472	0.89[ASN][1000 genomes]
rs6532577	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6821954	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840758	0.97[ASN][1000 genomes]
rs6842353	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6842388	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6842436	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6844037	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6848398	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848743	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659447	0.95[ASN][1000 genomes]
rs920155	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920157	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9998027	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[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	nsv997304	chr4:96575198-96861349	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1010830	chr4:96607025-96862878	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv537191	chr4:96607025-96862878	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv594915	chr4:96628653-97086618	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv428767	chr4:96676384-96831793	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv879628	chr4:96739251-96778499	Flanking Active TSS Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv879629	chr4:96747135-96818263	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:96756000-96758600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:96756800-96757000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:96756800-96757200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:96756800-96757200	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr4:96756800-96757200	Enhancers	Brain Substantia Nigra	brain

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