Variant report

Variant	rs440943
Chromosome Location	chr10:49457202-49457203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:49455171..49457750-chr10:49459859..49462154,2	K562	blood:
2	chr10:49455171..49459058-chr10:49459196..49462154,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN20C-7	chr10:49456586-49457221	NONHSAT013263

Variant related genes	Relation type
ENSG00000170324	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11101270	1.00[MEX][hapmap]
rs11816450	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12246849	1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs12262288	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1465605	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1652243	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1652245	1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs166815	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs166817	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17009533	1.00[JPT][hapmap]
rs1730444	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1730446	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1881733	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1881734	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs204006	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2455321	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2463958	1.00[ASN][1000 genomes]
rs2652408	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2698764	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs280605	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs280606	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs280608	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs280610	1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs280611	1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs280615	1.00[ASN][1000 genomes]
rs386570	1.00[ASW][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs399419	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs413065	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs426153	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs477693	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs477761	1.00[ASN][1000 genomes]
rs60503953	1.00[ASN][1000 genomes]
rs61840508	1.00[ASN][1000 genomes]
rs7073154	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7092864	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73294264	1.00[ASN][1000 genomes]
rs73296347	1.00[ASN][1000 genomes]
rs73296348	1.00[ASN][1000 genomes]
rs73296380	1.00[ASN][1000 genomes]
rs73296381	1.00[ASN][1000 genomes]
rs73296386	1.00[ASN][1000 genomes]
rs73296387	1.00[ASN][1000 genomes]
rs7915333	1.00[JPT][hapmap];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	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895367	chr10:49333754-49491047	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv895370	chr10:49421173-49484698	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49450800-49459400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr10:49451600-49459200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:49451800-49458200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:49451800-49459400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:49452000-49459400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr10:49454600-49457600	Enhancers	Right Ventricle	heart
7	chr10:49454800-49457800	Enhancers	Fetal Heart	heart
8	chr10:49455600-49458400	Enhancers	Fetal Thymus	thymus
9	chr10:49455800-49459400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr10:49456800-49458000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr10:49457000-49458200	Enhancers	Left Ventricle	heart
12	chr10:49457000-49458400	Enhancers	Right Atrium	heart
13	chr10:49457000-49459400	Weak transcription	GM12878-XiMat	blood
14	chr10:49457000-49460800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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