Variant report

Variant	rs654973
Chromosome Location	chr6:74270132-74270133
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:74269217..74272384-chr6:74272449..74274240,3	K562	blood:
2	chr6:74269117..74271723-chr6:74288666..74291103,2	K562	blood:
3	chr6:74225345..74228338-chr6:74268407..74270549,2	K562	blood:
4	chr6:74228296..74231283-chr6:74268216..74270797,2	K562	blood:
5	chr6:74228889..74230513-chr6:74269068..74271779,2	K562	blood:
6	chr6:74269349..74272192-chr6:74274693..74276750,2	K562	blood:

Variant related genes	Relation type
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1083740	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1083741	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12198468	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1245279	0.94[EUR][1000 genomes]
rs1245344	0.90[EUR][1000 genomes]
rs1245345	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1245346	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1245348	0.86[EUR][1000 genomes]
rs1390080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1691341	1.00[CEU][hapmap]
rs1713862	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1741895	1.00[CEU][hapmap]
rs1848523	1.00[CEU][hapmap]
rs1874231	1.00[CEU][hapmap]
rs2643196	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2753184	0.94[EUR][1000 genomes]
rs364734	1.00[CEU][hapmap]
rs371827	1.00[CEU][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs3757108	1.00[CEU][hapmap]
rs4079357	1.00[CEU][hapmap]
rs4708060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs472294	1.00[CEU][hapmap]
rs473078	1.00[CEU][hapmap]
rs476838	1.00[CEU][hapmap]
rs477431	0.86[EUR][1000 genomes]
rs479248	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs506262	1.00[CEU][hapmap]
rs516203	0.86[ASN][1000 genomes]
rs523883	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs535902	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs537379	0.90[EUR][1000 genomes]
rs541178	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs543642	1.00[CEU][hapmap]
rs605857	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs606263	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs608026	0.86[ASN][1000 genomes]
rs609829	1.00[CEU][hapmap]
rs621493	0.83[ASN][1000 genomes]
rs625478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs628732	0.90[EUR][1000 genomes]
rs636166	1.00[CEU][hapmap]
rs658475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs673511	1.00[CEU][hapmap]
rs674708	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs6907936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs7749897	0.86[ASN][1000 genomes]
rs7764560	1.00[CEU][hapmap]
rs780062	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs780063	0.86[EUR][1000 genomes]
rs780069	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs780070	0.88[EUR][1000 genomes]
rs9293930	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs9341424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9352000	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9352002	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9352007	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9360689	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9446952	1.00[CEU][hapmap]
rs951332	0.86[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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	esv2763576	chr6:74197638-74277249	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
9	nsv886159	chr6:74223153-74275405	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	159 gene(s)	inside rSNPs	diseases
10	nsv463153	chr6:74229258-74290291	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
11	nsv603693	chr6:74229258-74290291	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
12	nsv527357	chr6:74253266-74325403	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs654973	MTO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74266000-74275400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:74266600-74270400	Enhancers	HepG2	liver
3	chr6:74266800-74270400	Weak transcription	Brain Angular Gyrus	brain
4	chr6:74267200-74273800	Weak transcription	K562	blood
5	chr6:74267600-74270200	Weak transcription	Brain Anterior Caudate	brain
6	chr6:74267800-74270200	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:74268000-74270200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:74268200-74270200	Enhancers	GM12878-XiMat	blood
9	chr6:74268400-74270200	Weak transcription	A549	lung
10	chr6:74268600-74270200	Weak transcription	Brain Substantia Nigra	brain
11	chr6:74268600-74274600	Weak transcription	HSMMtube	muscle
12	chr6:74268800-74275400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:74269000-74270200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:74269000-74270200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:74269000-74270400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:74269000-74276800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:74269200-74270200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:74269200-74270200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:74269200-74270200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:74269200-74270400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr6:74269200-74275200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:74269400-74270400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:74269400-74275400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:74269800-74270400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:74269800-74270400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:74269800-74270600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr6:74269800-74270600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr6:74269800-74271000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:74269800-74271000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:74270000-74270400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:74270000-74270600	Enhancers	Duodenum Mucosa	Duodenum
32	chr6:74270000-74270600	Enhancers	NH-A	brain
33	chr6:74270000-74270800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr6:74270000-74270800	Enhancers	HUVEC	blood vessel
35	chr6:74270000-74271000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:74270000-74271000	Enhancers	Liver	Liver

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