Variant report

Variant	rs2894836
Chromosome Location	chr6:56250783-56250784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56246077..56248373-chr6:56250654..56253145,3	MCF-7	breast:
2	chr6:56241738..56245167-chr6:56250105..56253808,4	MCF-7	breast:
3	chr6:56249469..56251533-chr6:56299828..56301896,2	MCF-7	breast:
4	chr6:56250438..56252744-chr6:56257720..56260496,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124749	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1008768	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1008769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1008770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1014740	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1018414	0.98[ASN][1000 genomes]
rs1018415	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11968073	0.96[ASN][1000 genomes]
rs12205291	0.82[ASN][1000 genomes]
rs12528936	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13206552	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2143349	0.92[ASN][1000 genomes]
rs2179519	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2206528	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2206530	0.96[ASN][1000 genomes]
rs2397222	0.96[ASN][1000 genomes]
rs35253323	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4715621	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715624	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs629057	0.91[ASN][1000 genomes]
rs629506	0.91[ASN][1000 genomes]
rs643246	0.93[ASN][1000 genomes]
rs646884	0.93[ASN][1000 genomes]
rs669656	0.91[ASN][1000 genomes]
rs669728	0.91[ASN][1000 genomes]
rs926530	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9296843	0.93[ASN][1000 genomes]
rs9349821	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9370527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370530	0.93[ASN][1000 genomes]
rs9382625	0.89[ASN][1000 genomes]
rs9382627	0.96[ASN][1000 genomes]
rs9382630	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9396208	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9396209	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9942454	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[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

No data

Chromatin state (count:26 , 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	chr6:56241200-56252400	Weak transcription	Right Ventricle	heart
6	chr6:56244000-56251000	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:56244000-56252200	Weak transcription	Placenta	Placenta
8	chr6:56245600-56251600	Weak transcription	Stomach Mucosa	stomach
9	chr6:56245800-56252200	Enhancers	HepG2	liver
10	chr6:56247000-56251600	Weak transcription	Fetal Intestine Small	intestine
11	chr6:56247400-56251600	Weak transcription	Fetal Intestine Large	intestine
12	chr6:56247400-56263600	Weak transcription	Small Intestine	intestine
13	chr6:56247800-56252200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:56247800-56252200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:56247800-56252400	Weak transcription	Pancreas	Pancrea
16	chr6:56247800-56252600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:56247800-56252600	Weak transcription	HMEC	breast
18	chr6:56247800-56252600	Weak transcription	NHEK	skin
19	chr6:56249800-56252200	Weak transcription	Psoas Muscle	Psoas
20	chr6:56250000-56251600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:56250000-56252400	Weak transcription	Aorta	Aorta
22	chr6:56250000-56252400	Weak transcription	Gastric	stomach
23	chr6:56250000-56252600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:56250200-56251200	Weak transcription	Hela-S3	cervix
25	chr6:56250200-56253000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:56250600-56251200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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