Variant report

Variant	rs2206530
Chromosome Location	chr6:56246101-56246102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56241466..56244174-chr6:56245136..56247766,2	MCF-7	breast:
2	chr6:56246077..56248373-chr6:56250654..56253145,3	MCF-7	breast:
3	chr6:56243942..56247033-chr6:56303376..56305321,3	MCF-7	breast:
4	chr6:56239053..56241377-chr6:56244468..56246401,2	MCF-7	breast:
5	chr6:56241662..56247297-chr6:56405930..56409718,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1008768	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1008769	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1008770	0.99[ASN][1000 genomes]
rs1014740	0.89[ASN][1000 genomes]
rs1018414	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1018415	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11968073	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12528936	0.89[ASN][1000 genomes]
rs13206552	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2143349	0.85[CHB][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.91[ASN][1000 genomes]
rs2179519	0.91[ASN][1000 genomes]
rs2206528	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2397222	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2397223	0.86[CHB][hapmap]
rs2894836	0.96[ASN][1000 genomes]
rs35253323	0.86[ASN][1000 genomes]
rs4715621	0.91[ASN][1000 genomes]
rs4715624	0.86[ASN][1000 genomes]
rs629057	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs629506	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs643246	0.92[ASN][1000 genomes]
rs646884	0.90[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs669656	0.91[ASN][1000 genomes]
rs669728	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs926530	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296843	0.89[ASN][1000 genomes]
rs9349821	0.89[ASN][1000 genomes]
rs9370527	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs9370530	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9382625	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9382627	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9382630	0.86[ASN][1000 genomes]
rs9396208	0.89[ASN][1000 genomes]
rs9396209	0.89[ASN][1000 genomes]
rs9942454	0.89[ASN][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	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
rs2206530	COL21A1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56240400-56246400	Weak transcription	Fetal Intestine Large	intestine
2	chr6:56240400-56246800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:56240400-56247400	Weak transcription	Pancreas	Pancrea
4	chr6:56240400-56252400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:56240600-56247400	Weak transcription	Aorta	Aorta
6	chr6:56240600-56252200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:56240600-56252400	Weak transcription	Left Ventricle	heart
8	chr6:56240800-56251200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:56241000-56246400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:56241200-56249000	Weak transcription	Psoas Muscle	Psoas
11	chr6:56241200-56249600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:56241200-56252400	Weak transcription	Right Ventricle	heart
13	chr6:56243800-56246600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:56244000-56246600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:56244000-56250200	Enhancers	Hela-S3	cervix
16	chr6:56244000-56251000	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:56244000-56252200	Weak transcription	Placenta	Placenta
18	chr6:56244200-56246400	Weak transcription	HMEC	breast
19	chr6:56244200-56246600	Weak transcription	NHEK	skin
20	chr6:56244400-56246600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:56244400-56246600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:56244600-56246600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:56245400-56248600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:56245600-56249600	Weak transcription	Adipose Nuclei	Adipose
25	chr6:56245600-56251600	Weak transcription	Stomach Mucosa	stomach
26	chr6:56245800-56252200	Enhancers	HepG2	liver

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