Variant report

Variant	rs28401552
Chromosome Location	chr10:43700124-43700125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr10:43700080-43700230	HCT-116	colon:	n/a	n/a
2	CTCF	chr10:43700080-43700230	GM12873	blood:	n/a	n/a
3	CTCF	chr10:43700000-43700150	HFF-Myc	foreskin:	n/a	n/a
4	CTCF	chr10:43700110-43701142	A549	lung:	n/a	chr10:43700741-43700750
5	CTCF	chr10:43700040-43700190	HA-sp	spinal cord:	n/a	n/a
6	CTCF	chr10:43700100-43700250	NHDF-neo	bronchial:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:43698957..43702295-chr10:43702554..43706038,5	K562	blood:
2	chr10:43696369..43700743-chr10:43891529..43894634,3	K562	blood:
3	chr10:43696835..43700131-chr10:43902185..43905182,4	K562	blood:
4	chr10:43632409..43636039-chr10:43698014..43700588,4	K562	blood:
5	chr10:43699342..43701842-chr10:43722370..43724384,2	K562	blood:
6	chr10:43632694..43635237-chr10:43697053..43700182,3	MCF-7	breast:
7	chr10:43632409..43636039-chr10:43698014..43700588,6	K562	blood:
8	chr10:43700022..43701253-chr10:43750988..43751917,9	MCF-7	breast:
9	chr10:43698632..43700457-chr10:43704012..43705797,2	K562	blood:
10	chr10:43697420..43700683-chr10:43890424..43894292,4	K562	blood:

No data

Variant related genes	Relation type
RASGEF1A	TF binding region
ENSG00000169826	Chromatin interaction
ENSG00000273008	Chromatin interaction
ENSG00000169813	Chromatin interaction
ENSG00000198915	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10159558	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238441	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11238465	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258585	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12260994	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12262152	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12765436	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12765715	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12765838	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12766298	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12775330	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12775743	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12779732	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17363630	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799939	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1800863	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1864393	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879298	0.80[EUR][1000 genomes]
rs1879299	0.85[AMR][1000 genomes]
rs2075911	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2900627	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3026776	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3026779	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3026781	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3026782	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34817887	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4987091	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66557659	0.84[AMR][1000 genomes]
rs7074319	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086299	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092548	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096367	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71505665	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71505667	0.93[ASN][1000 genomes]
rs71505668	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72783237	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72783242	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7893332	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7903283	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910648	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910805	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921281	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7923256	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9804209	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	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
3	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1831010	chr10:43674916-43759185	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv895084	chr10:43688505-43765485	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv466881	chr10:43695049-43799588	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv550696	chr10:43695049-43799588	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv895085	chr10:43695049-43804617	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43675600-43700600	Weak transcription	A549	lung
2	chr10:43698000-43700200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr10:43698000-43700400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:43698000-43700400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr10:43698000-43700600	Weak transcription	Brain Angular Gyrus	brain
6	chr10:43698000-43722800	Weak transcription	Gastric	stomach
7	chr10:43698200-43700200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr10:43698200-43700400	Weak transcription	Brain Anterior Caudate	brain
9	chr10:43698200-43700600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr10:43698200-43700600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:43698200-43706600	Weak transcription	Brain Hippocampus Middle	brain
12	chr10:43698200-43707400	Weak transcription	Brain Substantia Nigra	brain
13	chr10:43698400-43700200	Weak transcription	Stomach Mucosa	stomach
14	chr10:43698400-43700400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:43698400-43700400	Weak transcription	Fetal Brain Female	brain
16	chr10:43698400-43700600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr10:43698400-43700600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:43698400-43700800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:43698400-43701200	Weak transcription	Brain Germinal Matrix	brain
20	chr10:43698400-43701400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr10:43698400-43706200	Weak transcription	HMEC	breast
22	chr10:43698400-43710800	Weak transcription	Esophagus	oesophagus
23	chr10:43698600-43700600	Enhancers	Spleen	Spleen
24	chr10:43699000-43700400	Weak transcription	Thymus	Thymus
25	chr10:43699000-43700600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:43699200-43700200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr10:43699200-43700200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr10:43699200-43700400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:43699200-43700400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:43699200-43700400	Weak transcription	Pancreas	Pancrea
31	chr10:43699200-43700600	Weak transcription	Right Ventricle	heart
32	chr10:43699200-43704200	Weak transcription	Fetal Thymus	thymus
33	chr10:43699400-43700200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr10:43699400-43700400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr10:43699400-43700400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr10:43699400-43700800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr10:43699400-43700800	Enhancers	H1 Cell Line	embryonic stem cell
38	chr10:43699400-43700800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr10:43699400-43700800	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr10:43699400-43701000	Enhancers	K562	blood
41	chr10:43699400-43701200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr10:43699400-43703200	Enhancers	Placenta	Placenta
43	chr10:43699400-43716800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr10:43699400-43724600	Weak transcription	Right Atrium	heart
45	chr10:43699800-43700400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr10:43699800-43702800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr10:43700000-43700200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr10:43700000-43700600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr10:43700000-43700800	Enhancers	Primary B cells from peripheral blood	blood
50	chr10:43700000-43701000	Weak transcription	Lung	lung

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