Variant report

Variant	rs11117669
Chromosome Location	chr1:216918975-216918976
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	chr1:216913734..216915380-chr1:216918408..216920801,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10863269	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11117667	0.87[YRI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11117668	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12059942	1.00[ASN][1000 genomes]
rs12070175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12402813	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403401	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339350	0.94[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17043436	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs17043466	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs17043570	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17043610	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066108	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2789721	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2789722	0.85[CHB][hapmap]
rs2789732	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2789733	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2813666	0.86[CHB][hapmap]
rs2813711	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2820875	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2820876	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2820881	1.00[CHB][hapmap]
rs2820882	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2999503	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2999504	0.83[CHD][hapmap]
rs61318304	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819764	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61819766	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61819772	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508694	chr1:216901014-216923883	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11117669	TGFB2	cis	cerebellum	SCAN
rs11117669	SMYD2	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216897400-216958600	Weak transcription	Pancreas	Pancrea
2	chr1:216911600-216934200	Weak transcription	Psoas Muscle	Psoas
3	chr1:216914400-216923400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:216916800-216921600	Weak transcription	Fetal Heart	heart
5	chr1:216918600-216919000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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