Variant report

Variant	rs1953798
Chromosome Location	chr14:70954149-70954150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:70952948..70955035-chr22:17637701..17639534,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10483830	0.87[CEU][hapmap]
rs12232170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12436902	0.91[EUR][1000 genomes]
rs12586325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12586328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17107997	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17108107	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs17108176	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17108246	0.87[CEU][hapmap]
rs17108264	0.87[CEU][hapmap]
rs17108274	0.87[CEU][hapmap]
rs17113651	0.87[CEU][hapmap]
rs1953802	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1959483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1959484	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1959485	0.80[CHD][hapmap]
rs1959486	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095807	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293877	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2332389	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34512695	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4143920	0.86[CHB][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap]
rs4899354	0.80[CHD][hapmap]
rs4902817	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs4902827	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56778245	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56824265	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57146008	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61671382	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7143655	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7145265	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7152771	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7154884	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7159432	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73293909	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73293935	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8014252	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs8014338	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8015163	0.91[EUR][1000 genomes]
rs8017584	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8021308	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv565042	chr14:70951234-71011734	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1050615	chr14:70954149-71013235	Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2763072	chr14:70954149-71013247	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1953798	ADAM20	cis	cerebellum	SCAN
rs1953798	SLC8A3	cis	cerebellum	SCAN
rs1953798	MAP3K9	cis	cerebellum	SCAN
rs1953798	MED6	cis	parietal	SCAN
rs1953798	PLEKHH1	cis	parietal	SCAN
rs1953798	MED6	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70910600-70955600	Weak transcription	Left Ventricle	heart
2	chr14:70948000-70955000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr14:70949000-70956000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr14:70949200-70956400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr14:70949400-70956200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr14:70951200-70956200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr14:70951400-70955000	Weak transcription	Aorta	Aorta
8	chr14:70951400-70957600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr14:70953800-70954200	Active TSS	Fetal Heart	heart

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