Variant report

Variant	rs10498892
Chromosome Location	chr6:74280784-74280785
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:74278735..74283200-chr6:74288390..74290564,5	K562	blood:
2	chr6:74230653..74233230-chr6:74279023..74281094,2	MCF-7	breast:
3	chr6:74227140..74231865-chr6:74277040..74281960,6	K562	blood:
4	chr6:74227140..74235678-chr6:74271460..74282263,27	K562	blood:
5	chr6:74233242..74235522-chr6:74280343..74281845,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156508	Chromatin interaction
ENSG00000229862	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10455281	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs10943112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10943113	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs10943117	0.86[ASN][1000 genomes]
rs11962999	0.86[EUR][1000 genomes]
rs11964414	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966187	0.83[EUR][1000 genomes]
rs12191488	0.81[EUR][1000 genomes]
rs12193002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12195068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12195584	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196281	0.86[ASN][1000 genomes]
rs12197318	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12199430	0.82[EUR][1000 genomes]
rs12203363	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12206052	0.83[EUR][1000 genomes]
rs12210126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12210394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12210825	0.86[ASN][1000 genomes]
rs12211279	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12212297	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213067	0.86[ASN][1000 genomes]
rs12213868	0.86[ASN][1000 genomes]
rs12214877	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs12216092	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13193629	0.86[ASN][1000 genomes]
rs13202151	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs13203297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13207999	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13211453	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13212809	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2351118	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2351119	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2351120	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2351121	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34342150	0.80[ASN][1000 genomes]
rs34613232	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35256309	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35468063	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35659919	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35733187	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36131846	0.86[ASN][1000 genomes]
rs3734518	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3757109	0.86[ASN][1000 genomes]
rs3757111	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3799288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4708064	0.84[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4708065	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59383274	0.86[ASN][1000 genomes]
rs62438456	0.86[ASN][1000 genomes]
rs62440462	0.86[ASN][1000 genomes]
rs71573599	0.81[EUR][1000 genomes]
rs72949387	0.86[ASN][1000 genomes]
rs7744053	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
9	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
10	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
11	nsv603694	chr6:74275405-74365807	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10498892	OGFRL1	cis	parietal	SCAN
rs10498892	EEF1A1	cis	parietal	SCAN
rs10498892	MTO1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74276400-74287800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:74277200-74280800	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:74277200-74280800	Weak transcription	K562	blood
4	chr6:74277200-74287200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:74277200-74287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:74277200-74287600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:74277200-74288600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:74277400-74280800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:74277800-74280800	Weak transcription	Liver	Liver
10	chr6:74278200-74280800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:74278200-74288600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:74278400-74281400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:74279000-74280800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:74280200-74281800	Enhancers	Fetal Heart	heart
15	chr6:74280600-74280800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:74280600-74280800	Enhancers	HSMMtube	muscle
17	chr6:74280600-74281000	Enhancers	Right Atrium	heart
18	chr6:74280600-74281200	Enhancers	Psoas Muscle	Psoas
19	chr6:74280600-74281200	Enhancers	A549	lung
20	chr6:74280600-74281200	Enhancers	HepG2	liver
21	chr6:74280600-74281200	Enhancers	HSMM	muscle
22	chr6:74280600-74281600	Enhancers	Left Ventricle	heart
23	chr6:74280600-74281600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr6:74280600-74281600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr6:74280600-74282200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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