Variant report

Variant	rs557675
Chromosome Location	chr11:65566719-65566720
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65563461..65568166-chr11:65728932..65730847,4	MCF-7	breast:
2	chr11:65560729..65563509-chr11:65565299..65568101,3	K562	blood:

Variant related genes	Relation type
ENSG00000175467	Chromatin interaction
ENSG00000172818	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12797706	0.81[ASN][1000 genomes]
rs2276133	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs3814707	0.91[CHB][hapmap];0.85[YRI][hapmap]
rs44205	0.95[GIH][hapmap]
rs642803	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs644740	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
4	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs557675	CTSF	cis	cerebellum	SCAN
rs557675	PCNXL3	cis	cerebellum	SCAN
rs557675	SNX32	cis	parietal	SCAN
rs557675	DRAP1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65558200-65568800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr11:65559800-65570600	Weak transcription	Spleen	Spleen
3	chr11:65562800-65568600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr11:65563400-65567600	Weak transcription	Gastric	stomach
5	chr11:65563400-65576200	Weak transcription	Pancreas	Pancrea
6	chr11:65563800-65566800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:65563800-65566800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:65563800-65571000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:65564200-65566800	Enhancers	Placenta	Placenta
10	chr11:65565200-65568600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:65565400-65568800	Weak transcription	Fetal Intestine Large	intestine
12	chr11:65565600-65568800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:65565600-65569000	Weak transcription	Fetal Intestine Small	intestine
14	chr11:65565600-65571400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:65565600-65571400	Weak transcription	Esophagus	oesophagus
16	chr11:65565600-65577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:65566200-65566800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr11:65566200-65566800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr11:65566200-65566800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr11:65566600-65566800	Enhancers	H9 Cell Line	embryonic stem cell
21	chr11:65566600-65568800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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