Variant report

Variant	rs12209310
Chromosome Location	chr6:150226018-150226019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150157068..150159142-chr6:150224629..150226824,2	MCF-7	breast:
2	chr6:150225385..150227618-chr6:150231399..150233931,2	MCF-7	breast:
3	chr6:150182462..150186110-chr6:150225717..150228741,3	MCF-7	breast:
4	chr6:150222304..150224162-chr6:150225800..150228066,2	MCF-7	breast:
5	chr6:150195717..150198563-chr6:150225615..150228061,2	K562	blood:

Variant related genes	Relation type
ENSG00000268592	Chromatin interaction
ENSG00000120256	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10457852	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12204653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12210822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527391	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12528243	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1855572	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1999632	0.94[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1999633	0.88[CEU][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2342766	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3798763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3922946	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3922947	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4473864	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4869755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4869756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4869767	0.92[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4869768	0.92[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4870078	1.00[CEU][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4870110	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4870117	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4870118	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5024811	0.85[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57894361	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6557165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912330	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7452592	0.85[EUR][1000 genomes]
rs7764677	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs915140	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9322229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9371228	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9383941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9397070	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12209310	LRP11	cis	cerebellum	SCAN
rs12209310	LRP11	cis	parietal	SCAN
rs12209310	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs12209310	RP11-350J20.5	cis	lung	GTEx
rs12209310	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs12209310	SHPRH	cis	cerebellum	SCAN
rs12209310	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs12209310	LATS1	cis	cerebellum	SCAN
rs12209310	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs12209310	RAET1G	cis	Thyroid	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150218800-150227600	Weak transcription	Fetal Intestine Small	intestine
2	chr6:150219200-150226200	Weak transcription	Spleen	Spleen
3	chr6:150222600-150226600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:150222600-150229800	Weak transcription	Pancreas	Pancrea
5	chr6:150223000-150226600	Weak transcription	Esophagus	oesophagus
6	chr6:150225200-150227400	Enhancers	Fetal Muscle Leg	muscle
7	chr6:150225400-150226200	Enhancers	Stomach Smooth Muscle	stomach
8	chr6:150225400-150227200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr6:150225400-150227600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr6:150225400-150227800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr6:150225600-150226400	Weak transcription	Right Ventricle	heart
12	chr6:150225800-150226200	Enhancers	Right Atrium	heart
13	chr6:150226000-150227800	Enhancers	Lung	lung

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