Variant report

Variant	rs17221823
Chromosome Location	chr20:40789061-40789062
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:40782305..40784731-chr20:40788079..40790643,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17221067	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs17221137	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs17221326	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17312515	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs2903466	0.85[CEU][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4281967	0.82[CHB][hapmap]
rs55789113	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55796708	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55889296	0.83[AMR][1000 genomes]
rs56039253	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56256174	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56284628	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59610476	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6016698	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6030012	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6030014	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6102693	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6102696	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6513775	0.86[JPT][hapmap]
rs73114444	0.80[AMR][1000 genomes]
rs73114449	0.81[ASN][1000 genomes]
rs73118438	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73120412	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73120420	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73120444	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17221823	CTNNBL1	cis	cerebellum	SCAN
rs17221823	KCNS1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40788000-40789400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr20:40788200-40790000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
3	chr20:40788400-40789400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr20:40788600-40789200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr20:40788600-40789800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr20:40788600-40790200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr20:40788600-40790800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr20:40788800-40789400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr20:40789000-40789600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr20:40789000-40789600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
11	chr20:40789000-40789600	Enhancers	Fetal Stomach	stomach

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