Variant report

Variant	rs55855950
Chromosome Location	chr10:98917358-98917359
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	NFIC	chr10:98917280-98918230	GM12878	blood:	n/a	n/a
2	CEBPD	chr10:98917277-98917600	HepG2	liver:	n/a	n/a
3	MYC	chr10:98917351-98917677	HepG2	liver:	n/a	n/a
4	PAX5	chr10:98917257-98917752	GM12878	blood:	n/a	n/a
5	ELF1	chr10:98917300-98917774	HepG2	liver:	n/a	n/a
6	ELF1	chr10:98917235-98917649	GM12878	blood:	n/a	n/a
7	ELF1	chr10:98917314-98917794	HepG2	liver:	n/a	n/a
8	REST	chr10:98917299-98917683	HepG2	liver:	n/a	chr10:98917391-98917404 chr10:98917398-98917406
9	IRF4	chr10:98917309-98917867	GM12878	blood:	n/a	n/a
10	JUND	chr10:98917333-98917695	HepG2	liver:	n/a	chr10:98917468-98917479
11	RAD21	chr10:98917292-98917800	HepG2	liver:	n/a	n/a
12	NR2F2	chr10:98917059-98918203	HepG2	liver:	n/a	n/a
13	FOXA1	chr10:98917255-98917747	HepG2	liver:	n/a	n/a
14	TEAD4	chr10:98917157-98917699	HepG2	liver:	n/a	n/a
15	FOXA1	chr10:98917262-98917706	HepG2	liver:	n/a	n/a
16	ZNF143	chr10:98917322-98917725	GM12878	blood:	n/a	n/a
17	CHD2	chr10:98917333-98917693	GM12878	blood:	n/a	n/a
18	RCOR1	chr10:98917224-98917583	HepG2	liver:	n/a	n/a
19	MYBL2	chr10:98917124-98917718	HepG2	liver:	n/a	n/a
20	IRF4	chr10:98917311-98917847	GM12878	blood:	n/a	n/a
21	PAX5	chr10:98917354-98917750	GM12878	blood:	n/a	n/a
22	RAD21	chr10:98917310-98917721	HepG2	liver:	n/a	n/a
23	MYBL2	chr10:98917214-98918116	HepG2	liver:	n/a	n/a
24	HDAC2	chr10:98917204-98917765	HepG2	liver:	n/a	n/a
25	EP300	chr10:98917310-98917777	HepG2	liver:	n/a	n/a
26	EP300	chr10:98917163-98917842	HepG2	liver:	n/a	n/a
27	MAX	chr10:98917095-98918086	HepG2	liver:	n/a	n/a
28	RAD21	chr10:98917325-98917706	HepG2	liver:	n/a	n/a
29	FOXA1	chr10:98917290-98917668	HepG2	liver:	n/a	n/a
30	HNF4A	chr10:98917251-98917607	HepG2	liver:	n/a	chr10:98917460-98917482
31	FOXA2	chr10:98917247-98917718	HepG2	liver:	n/a	n/a
32	EBF1	chr10:98917153-98917608	GM12878	blood:	n/a	n/a
33	FOXA1	chr10:98917217-98917764	HepG2	liver:	n/a	n/a
34	HNF4G	chr10:98917244-98917705	HepG2	liver:	n/a	chr10:98917460-98917482
35	RXRA	chr10:98917314-98917687	HepG2	liver:	n/a	n/a
36	RELA	chr10:98917248-98918027	GM12878	blood:	n/a	n/a
37	HDAC2	chr10:98917193-98917742	HepG2	liver:	n/a	n/a
38	MBD4	chr10:98917203-98917949	HepG2	liver:	n/a	n/a
39	RUNX3	chr10:98917221-98917996	GM12878	blood:	n/a	n/a
40	MXI1	chr10:98917237-98917715	HepG2	liver:	n/a	n/a
41	NFIC	chr10:98917214-98917783	HepG2	liver:	n/a	n/a
42	POLR2A	chr10:98917244-98917995	HepG2	liver:	n/a	n/a
43	RUNX3	chr10:98917126-98918209	GM12878	blood:	n/a	n/a
44	NR2F2	chr10:98917154-98917826	HepG2	liver:	n/a	n/a
45	EBF1	chr10:98917338-98917757	GM12878	blood:	n/a	n/a
46	MTA3	chr10:98917248-98918167	GM12878	blood:	n/a	n/a
47	TBP	chr10:98917292-98918019	HepG2	liver:	n/a	n/a
48	EP300	chr10:98917343-98917940	HepG2	liver:	n/a	n/a
49	NFIC	chr10:98917205-98917811	HepG2	liver:	n/a	n/a
50	HNF4A	chr10:98917293-98917590	HepG2	liver:	n/a	chr10:98917460-98917482

Variant related genes	Relation type
ARHGAP19-SLIT1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10437452	1.00[ASN][1000 genomes]
rs11188978	1.00[ASN][1000 genomes]
rs11188999	1.00[ASN][1000 genomes]
rs12240946	1.00[ASN][1000 genomes]
rs12241405	1.00[ASN][1000 genomes]
rs12241564	1.00[ASN][1000 genomes]
rs12254525	1.00[ASN][1000 genomes]
rs56327223	1.00[ASN][1000 genomes]
rs57501540	1.00[ASN][1000 genomes]
rs7071211	1.00[ASN][1000 genomes]
rs7073150	1.00[ASN][1000 genomes]
rs7081197	1.00[ASN][1000 genomes]
rs7082838	1.00[ASN][1000 genomes]
rs7086875	1.00[ASN][1000 genomes]
rs7090441	1.00[ASN][1000 genomes]
rs7090690	1.00[ASN][1000 genomes]
rs72821721	1.00[ASN][1000 genomes]
rs72821744	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72821759	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73320607	1.00[ASN][1000 genomes]
rs7893325	1.00[ASN][1000 genomes]
rs7906294	1.00[ASN][1000 genomes]
rs7920238	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv2758236	chr10:98789963-98962472	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2759777	chr10:98789963-98962472	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv7506	chr10:98902440-98940209	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr10:98901000-98923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:98901400-98918400	Weak transcription	Brain Angular Gyrus	brain
3	chr10:98904600-98917400	Weak transcription	Brain Anterior Caudate	brain
4	chr10:98904600-98922800	Weak transcription	Fetal Brain Male	brain
5	chr10:98907800-98922800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr10:98910400-98917800	Strong transcription	Brain Germinal Matrix	brain
7	chr10:98910600-98923400	Weak transcription	Fetal Lung	lung
8	chr10:98911000-98923200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:98911200-98917400	Strong transcription	Fetal Brain Female	brain
10	chr10:98912200-98917800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:98912400-98917400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:98913200-98923400	Weak transcription	Fetal Stomach	stomach
13	chr10:98914200-98918600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr10:98914600-98917400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:98916000-98922400	Weak transcription	Thymus	Thymus
16	chr10:98916000-98923400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:98917200-98917400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr10:98917200-98917600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:98917200-98917600	Enhancers	GM12878-XiMat	blood
20	chr10:98917200-98918000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:98917200-98918000	Enhancers	Primary B cells from peripheral blood	blood
22	chr10:98917200-98918000	Flanking Active TSS	HepG2	liver
23	chr10:98917200-98923400	Genic enhancers	Fetal Thymus	thymus

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