Variant report

Variant	rs12202464
Chromosome Location	chr6:56247749-56247750
allele	C/G
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	chr6:56247082..56250029-chr6:56297051..56298820,2	MCF-7	breast:
4	chr6:56246501..56248507-chr6:56300256..56301859,2	MCF-7	breast:
5	chr6:56246730..56249107-chr6:56300637..56303346,3	MCF-7	breast:
6	chr6:56241805..56244014-chr6:56247692..56249207,2	MCF-7	breast:
7	chr6:56247738..56250356-chr6:56304271..56306407,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000220666	Chromatin interaction
ENSG00000266793	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10456187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10456733	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10456734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10949000	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12214233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28855739	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55780935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62412409	1.00[AFR][1000 genomes]
rs62412458	0.91[AMR][1000 genomes];0.94[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	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

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56240400-56252400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:56240600-56252200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:56240600-56252400	Weak transcription	Left Ventricle	heart
4	chr6:56240800-56251200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:56241200-56249000	Weak transcription	Psoas Muscle	Psoas
6	chr6:56241200-56249600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:56241200-56252400	Weak transcription	Right Ventricle	heart
8	chr6:56244000-56250200	Enhancers	Hela-S3	cervix
9	chr6:56244000-56251000	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:56244000-56252200	Weak transcription	Placenta	Placenta
11	chr6:56245400-56248600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:56245600-56249600	Weak transcription	Adipose Nuclei	Adipose
13	chr6:56245600-56251600	Weak transcription	Stomach Mucosa	stomach
14	chr6:56245800-56252200	Enhancers	HepG2	liver
15	chr6:56246400-56247800	Enhancers	HMEC	breast
16	chr6:56246600-56247800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:56246600-56247800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:56246600-56247800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:56246600-56247800	Enhancers	NHEK	skin
20	chr6:56246800-56247800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:56247000-56251600	Weak transcription	Fetal Intestine Small	intestine
22	chr6:56247400-56247800	Enhancers	Pancreas	Pancrea
23	chr6:56247400-56250600	Weak transcription	HSMMtube	muscle
24	chr6:56247400-56251600	Weak transcription	Fetal Intestine Large	intestine
25	chr6:56247400-56263600	Weak transcription	Small Intestine	intestine
26	chr6:56247600-56247800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:56247600-56248800	Weak transcription	Aorta	Aorta

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