Variant report

Variant	rs10882899
Chromosome Location	chr10:99095945-99095946
allele	C/G
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	FOS	chr10:99095869-99096851	MCF10A-Er-Src	breast:	n/a	chr10:99096437-99096451 chr10:99096768-99096776
2	CEBPB	chr10:99095823-99096023	HepG2	liver:	n/a	chr10:99095963-99095974 chr10:99095963-99095974
3	MYC	chr10:99095739-99096753	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr10:99095788-99096020	A549	lung:	n/a	chr10:99095963-99095974 chr10:99095963-99095974
5	POLR2A	chr10:99095786-99096950	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr10:99095863-99097086	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr10:99095818-99097147	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:99095023..99098677-chr10:99109833..99114591,4	MCF-7	breast:
2	chr10:99095422..99098240-chr10:99107284..99109589,2	MCF-7	breast:
3	chr10:99049975..99053832-chr10:99093402..99096465,5	K562	blood:
4	chr10:99069668..99072343-chr10:99094033..99096294,2	MCF-7	breast:
5	chr10:99094972..99096841-chr10:99101105..99102688,2	MCF-7	breast:
6	chr10:99095891..99098123-chr10:99100617..99102682,2	K562	blood:
7	chr10:99094747..99096526-chr10:99120700..99122428,2	MCF-7	breast:
8	chr10:99091712..99094616-chr10:99095407..99097123,2	K562	blood:
9	chr10:99048545..99053546-chr10:99092341..99096465,6	K562	blood:

Variant related genes	Relation type
FRAT2	TF binding region
ENSG00000237169	Chromatin interaction
ENSG00000225850	Chromatin interaction
ENSG00000269891	Chromatin interaction
ENSG00000181274	Chromatin interaction
ENSG00000213390	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10736116	0.85[EUR][1000 genomes]
rs10748694	0.86[EUR][1000 genomes]
rs10786324	0.86[EUR][1000 genomes]
rs10786325	0.81[EUR][1000 genomes]
rs10786326	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10786327	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10786329	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10786330	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10786332	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10786333	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786334	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786335	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882883	0.82[EUR][1000 genomes]
rs10882884	0.82[EUR][1000 genomes]
rs10882889	0.85[EUR][1000 genomes]
rs10882891	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10882894	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10882897	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882898	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189100	0.80[EUR][1000 genomes]
rs11189120	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11189122	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11189127	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11189131	0.87[EUR][1000 genomes]
rs11189132	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189137	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189138	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12221430	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12413688	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12571098	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1334892	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1890966	0.97[ASN][1000 genomes]
rs3740512	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3740522	0.82[EUR][1000 genomes]
rs3781373	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4917766	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4919087	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4919089	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4919090	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4919091	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61863767	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6584116	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7067835	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7072078	0.82[EUR][1000 genomes]
rs7076523	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7078288	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7080275	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7901853	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs945187	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs945189	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak 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	27 gene(s)	inside rSNPs	diseases
4	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv825533	chr10:99070570-99115599	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS 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
7	nsv825534	chr10:99081505-99115599	Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99094400-99096000	Active TSS	Primary hematopoietic stem cells	blood
2	chr10:99094800-99096600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:99095200-99096000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr10:99095200-99096200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr10:99095200-99096400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr10:99095200-99096800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:99095200-99096800	Weak transcription	Ovary	ovary
8	chr10:99095200-99097200	Weak transcription	Esophagus	oesophagus
9	chr10:99095200-99097400	Enhancers	Stomach Mucosa	stomach
10	chr10:99095200-99097600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr10:99095200-99097600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:99095200-99109400	Weak transcription	HSMMtube	muscle
13	chr10:99095200-99115200	Weak transcription	Gastric	stomach
14	chr10:99095400-99096000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:99095400-99096000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr10:99095400-99096000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr10:99095400-99096000	Enhancers	NHEK	skin
18	chr10:99095400-99096400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr10:99095400-99096400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr10:99095400-99096600	Weak transcription	Adipose Nuclei	Adipose
21	chr10:99095400-99096600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:99095400-99096600	Weak transcription	Psoas Muscle	Psoas
23	chr10:99095400-99096600	Enhancers	Hela-S3	cervix
24	chr10:99095400-99096800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr10:99095400-99096800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr10:99095400-99096800	Weak transcription	Brain Hippocampus Middle	brain
27	chr10:99095400-99096800	Weak transcription	Brain Substantia Nigra	brain
28	chr10:99095400-99096800	Weak transcription	Right Atrium	heart
29	chr10:99095400-99096800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:99095400-99096800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr10:99095400-99097000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr10:99095400-99097200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr10:99095400-99097200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr10:99095400-99097200	Weak transcription	Aorta	Aorta
35	chr10:99095400-99097200	Enhancers	Brain Anterior Caudate	brain
36	chr10:99095400-99097200	Weak transcription	Colonic Mucosa	Colon
37	chr10:99095400-99097200	Weak transcription	Lung	lung
38	chr10:99095400-99097200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr10:99095400-99097200	Enhancers	HepG2	liver
40	chr10:99095400-99097400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr10:99095400-99097400	Enhancers	A549	lung
42	chr10:99095400-99097600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr10:99095400-99097600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:99095400-99098000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr10:99095400-99098000	Enhancers	Placenta	Placenta
46	chr10:99095400-99098200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr10:99095400-99098600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr10:99095400-99109400	Weak transcription	Liver	Liver
49	chr10:99095400-99115600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr10:99095400-99115600	Weak transcription	Left Ventricle	heart

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