Variant report

Variant	rs6941846
Chromosome Location	chr6:56302621-56302622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr6:56302129-56302823	ECC-1	luminal epithelium:	n/a	n/a
2	STAT3	chr6:56302090-56302718	MCF10A-Er-Src	breast:	n/a	chr6:56302488-56302502 chr6:56302520-56302531 chr6:56302491-56302500 chr6:56302490-56302499 chr6:56302522-56302530 chr6:56302489-56302500 chr6:56302336-56302350
3	E2F4	chr6:56302511-56302662	MCF10A-Er-Src	breast:	n/a	n/a
4	EP300	chr6:56302307-56302721	SK-N-SH_RA	brain:	n/a	n/a
5	NR3C1	chr6:56302266-56302719	ECC-1	luminal epithelium:	n/a	n/a
6	STAT3	chr6:56301874-56303142	MCF10A-Er-Src	breast:	n/a	chr6:56302488-56302502 chr6:56302520-56302531 chr6:56302491-56302500 chr6:56302490-56302499 chr6:56302522-56302530 chr6:56302489-56302500 chr6:56302336-56302350
7	EP300	chr6:56302247-56302786	ECC-1	luminal epithelium:	n/a	n/a
8	BRCA1	chr6:56302399-56302650	Hela-S3	cervix:	n/a	n/a
9	TEAD4	chr6:56302118-56302858	ECC-1	luminal epithelium:	n/a	n/a
10	EP300	chr6:56302052-56302853	ECC-1	luminal epithelium:	n/a	chr6:56302210-56302224
11	MYC	chr6:56302261-56302662	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT1	chr6:56302019-56302864	Hela-S3	cervix:	n/a	chr6:56302488-56302502 chr6:56302491-56302500 chr6:56302490-56302499 chr6:56302522-56302530 chr6:56302336-56302350
13	FOS	chr6:56302319-56302699	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr6:56302259-56302708	MCF10A-Er-Src	breast:	n/a	n/a
15	NR3C1	chr6:56302240-56302671	ECC-1	luminal epithelium:	n/a	n/a
16	NFIC	chr6:56302098-56302846	ECC-1	luminal epithelium:	n/a	n/a
17	ESR1	chr6:56302168-56302776	ECC-1	luminal epithelium:	n/a	n/a
18	ESR1	chr6:56302230-56302691	ECC-1	luminal epithelium:	n/a	n/a
19	TEAD4	chr6:56302231-56302764	ECC-1	luminal epithelium:	n/a	n/a
20	TCF12	chr6:56302158-56302738	ECC-1	luminal epithelium:	n/a	n/a
21	TCF12	chr6:56302063-56302945	ECC-1	luminal epithelium:	n/a	n/a
22	ESR1	chr6:56302228-56302676	ECC-1	luminal epithelium:	n/a	n/a
23	MYC	chr6:56302369-56302679	MCF10A-Er-Src	breast:	n/a	n/a
24	FOXM1	chr6:56302154-56302888	ECC-1	luminal epithelium:	n/a	n/a
25	CEBPB	chr6:56302196-56302862	ECC-1	luminal epithelium:	n/a	n/a
26	NFIC	chr6:56301980-56302988	ECC-1	luminal epithelium:	n/a	n/a
27	STAT3	chr6:56302190-56303200	MCF10A-Er-Src	breast:	n/a	chr6:56302488-56302502 chr6:56302520-56302531 chr6:56302491-56302500 chr6:56302490-56302499 chr6:56302522-56302530 chr6:56302489-56302500 chr6:56302336-56302350
28	FOXA1	chr6:56302235-56302691	ECC-1	luminal epithelium:	n/a	n/a
29	ESR1	chr6:56302197-56302740	ECC-1	luminal epithelium:	n/a	n/a
30	FOS	chr6:56302336-56302685	MCF10A-Er-Src	breast:	n/a	n/a
31	EP300	chr6:56302297-56302671	SK-N-SH_RA	brain:	n/a	n/a
32	STAT3	chr6:56302169-56303603	MCF10A-Er-Src	breast:	n/a	chr6:56302488-56302502 chr6:56302520-56302531 chr6:56302491-56302500 chr6:56302490-56302499 chr6:56302522-56302530 chr6:56302489-56302500 chr6:56302336-56302350
33	STAT3	chr6:56302271-56302689	Hela-S3	cervix:	n/a	chr6:56302488-56302502 chr6:56302520-56302531 chr6:56302491-56302500 chr6:56302490-56302499 chr6:56302522-56302530 chr6:56302489-56302500 chr6:56302336-56302350
34	FOS	chr6:56302235-56302764	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:56238499..56241201-chr6:56301046..56303726,2	MCF-7	breast:
2	chr6:56295799..56298000-chr6:56302478..56305117,2	MCF-7	breast:
3	chr6:56298843..56301958-chr6:56302177..56305032,4	MCF-7	breast:
4	chr6:56302272..56304298-chr6:56305503..56307408,2	K562	blood:
5	chr6:56230309..56231813-chr6:56301567..56303735,2	MCF-7	breast:
6	chr6:56302578..56305844-chr6:56326114..56330070,4	MCF-7	breast:
7	chr6:56233493..56236499-chr6:56300077..56302694,3	MCF-7	breast:
8	chr6:56300059..56302914-chr6:56304069..56306007,3	MCF-7	breast:
9	chr6:56299637..56301821-chr6:56302113..56303860,2	K562	blood:
10	chr6:56246730..56249107-chr6:56300637..56303346,3	MCF-7	breast:

Variant related genes	Relation type
RCC2P7	TF binding region
ENSG00000151914	Chromatin interaction
ENSG00000266793	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10484787	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1323318	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1323319	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16887916	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2209037	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2224749	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2397225	0.80[AMR][1000 genomes]
rs6903211	0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs6915066	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6917087	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73465822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475698	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475702	1.00[JPT][hapmap]

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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6941846	COL21A1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56300200-56303000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:56300200-56303600	Enhancers	Liver	Liver
3	chr6:56300600-56303000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:56301000-56304400	Weak transcription	Fetal Intestine Large	intestine
5	chr6:56301000-56305200	Weak transcription	Pancreas	Pancrea
6	chr6:56301600-56303600	Enhancers	Hela-S3	cervix
7	chr6:56301800-56303200	Enhancers	HMEC	breast
8	chr6:56301800-56303200	Enhancers	NHEK	skin
9	chr6:56302000-56302800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:56302000-56303000	Enhancers	Colon Smooth Muscle	Colon
11	chr6:56302000-56303000	Enhancers	Stomach Mucosa	stomach
12	chr6:56302000-56303200	Enhancers	Rectal Smooth Muscle	rectum
13	chr6:56302200-56303000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:56302600-56303000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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