Variant report

Variant	rs2252804
Chromosome Location	chr10:43906945-43906946
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	POLR2A	chr10:43906737-43907481	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr10:43906879-43907042	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43901784..43908257-chr10:43928243..43934263,17	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF487P-4	chr10:43906922-43908086	NONHSAT012960

Variant related genes	Relation type
HNRNPF	TF binding region
ENSG00000243660	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10793430	0.86[ASN][1000 genomes]
rs10793431	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10793432	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10899798	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10899799	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1126487	0.86[ASN][1000 genomes]
rs12257917	0.90[AFR][1000 genomes]
rs1416226	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2066043	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2066044	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2247860	0.82[ASN][1000 genomes]
rs2248332	0.84[AFR][1000 genomes]
rs2248335	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2248469	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2248706	0.83[ASN][1000 genomes]
rs2251896	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2252783	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2252785	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2252800	0.92[AFR][1000 genomes]
rs2255967	0.90[AFR][1000 genomes]
rs2256495	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2256613	0.86[ASN][1000 genomes]
rs2265886	0.84[AFR][1000 genomes]
rs2492405	0.81[AFR][1000 genomes]
rs2492408	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2492409	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2492410	0.82[ASN][1000 genomes]
rs2492411	0.82[ASN][1000 genomes]
rs2492412	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2819021	0.81[ASN][1000 genomes]
rs2819032	0.91[AFR][1000 genomes]
rs2819034	0.90[AFR][1000 genomes]
rs2999276	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2999282	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2999287	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3000700	0.84[AFR][1000 genomes]
rs4584528	0.81[AFR][1000 genomes]
rs4597022	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56059584	0.90[AFR][1000 genomes]
rs7070769	0.86[ASN][1000 genomes]
rs7092599	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7894374	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7918726	0.86[ASN][1000 genomes]
rs7920539	0.86[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	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv825355	chr10:43890579-43923802	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv825356	chr10:43893080-43946515	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43905600-43913600	Weak transcription	Esophagus	oesophagus
2	chr10:43905800-43907400	Weak transcription	NHEK	skin
3	chr10:43905800-43911000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr10:43905800-43913400	Weak transcription	Fetal Intestine Small	intestine
5	chr10:43905800-43913800	Weak transcription	Stomach Mucosa	stomach
6	chr10:43905800-43915600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr10:43905800-43915600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr10:43906000-43907200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:43906000-43908000	Enhancers	HepG2	liver
10	chr10:43906000-43908600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr10:43906000-43915800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:43906200-43907400	Weak transcription	K562	blood
13	chr10:43906200-43907400	Weak transcription	NHDF-Ad	bronchial
14	chr10:43906200-43908600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr10:43906200-43908800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr10:43906200-43908800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr10:43906200-43911600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr10:43906200-43911600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr10:43906200-43911800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr10:43906200-43912000	Weak transcription	Dnd41	blood
21	chr10:43906200-43915200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:43906400-43915600	Weak transcription	Hela-S3	cervix
23	chr10:43906600-43907800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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