Variant report

Variant	rs2270933
Chromosome Location	chr5:126781446-126781447
allele	A/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	GATA3	chr5:126780878-126781487	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
MEGF10	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10491250	1.00[CEU][hapmap]
rs10519935	1.00[CEU][hapmap]
rs11241930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11745840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747639	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11950754	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11950816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12109001	1.00[CEU][hapmap]
rs1363386	1.00[CEU][hapmap]
rs1529468	1.00[CEU][hapmap]
rs1587628	0.83[EUR][1000 genomes]
rs1592960	0.83[EUR][1000 genomes]
rs17164854	1.00[CEU][hapmap]
rs17164922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17164923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17164951	1.00[CEU][hapmap]
rs17164957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17165013	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs17165018	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs17165019	1.00[CEU][hapmap]
rs17684644	1.00[CEU][hapmap]
rs17684655	1.00[CEU][hapmap]
rs17684679	1.00[CEU][hapmap]
rs17684691	1.00[CEU][hapmap]
rs17684740	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs17684775	1.00[CEU][hapmap]
rs17685202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17763126	1.00[CEU][hapmap]
rs17763172	1.00[CEU][hapmap]
rs1990954	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs1990955	1.00[CEU][hapmap]
rs2042942	1.00[CEU][hapmap]
rs2134252	0.83[EUR][1000 genomes]
rs2408871	0.81[YRI][hapmap]
rs3756721	0.85[YRI][hapmap]
rs3851468	1.00[CEU][hapmap]
rs41298320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55861432	0.83[EUR][1000 genomes]
rs57626860	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60681812	0.80[AFR][1000 genomes]
rs6595773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865700	1.00[CEU][hapmap]
rs6866275	1.00[CEU][hapmap]
rs6873921	1.00[CEU][hapmap]
rs6874260	1.00[CEU][hapmap]
rs6877383	1.00[CEU][hapmap]
rs6883445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897163	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73331215	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73348744	0.80[AFR][1000 genomes]
rs7737871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929781	1.00[CEU][hapmap]
rs929782	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126742800-126782000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:126742800-126792400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:126743000-126784800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:126761000-126783400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:126763400-126794000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:126765800-126782000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:126768200-126782000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:126774600-126798800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:126776000-126783200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:126776400-126785200	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:126776600-126782600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:126776600-126784600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:126777000-126782000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:126777000-126783200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:126777600-126783200	Weak transcription	NH-A	brain
16	chr5:126778000-126783200	Weak transcription	HSMM	muscle
17	chr5:126778000-126790800	Strong transcription	Fetal Muscle Leg	muscle
18	chr5:126778000-126795400	Weak transcription	Brain Angular Gyrus	brain
19	chr5:126778800-126783200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:126779000-126782000	Weak transcription	Brain Anterior Caudate	brain
21	chr5:126779000-126783200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:126779400-126783200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:126779600-126782200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:126779600-126782400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr5:126780800-126781800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:126780800-126782600	Enhancers	Brain Hippocampus Middle	brain
27	chr5:126781000-126781600	Enhancers	Brain Substantia Nigra	brain
28	chr5:126781000-126782400	Strong transcription	HSMMtube	muscle
29	chr5:126781000-126782600	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr5:126781200-126782800	Enhancers	Brain Cingulate Gyrus	brain
31	chr5:126781400-126782600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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