Variant report

Variant	rs55804343
Chromosome Location	chr6:39234907-39234908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39234576..39236394-chr6:39278908..39280593,2	MCF-7	breast:
2	chr6:39234314..39234951-chr6:39243222..39243766,2	MCF-7	breast:
3	chr6:39233505..39239976-chr6:39262109..39267318,6	MCF-7	breast:
4	chr6:39195043..39199102-chr6:39233396..39239186,7	MCF-7	breast:
5	chr6:39167435..39172891-chr6:39233498..39237624,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11759627	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961538	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758870	0.91[EUR][1000 genomes]
rs2758873	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758879	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758880	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2758886	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758896	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758902	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758903	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758905	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815033	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815034	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815043	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815047	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815059	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815060	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815062	0.91[EUR][1000 genomes]
rs4711589	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55812552	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55889689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56011317	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56300329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39224400-39238400	Weak transcription	Spleen	Spleen
2	chr6:39227200-39236000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:39230000-39235000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:39231400-39236600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:39231800-39235000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:39231800-39236000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:39231800-39236000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:39231800-39236400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:39231800-39236400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:39232000-39236000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:39232000-39236000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:39232000-39239800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:39233200-39236000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr6:39233400-39235000	Enhancers	Fetal Intestine Large	intestine
15	chr6:39233600-39240200	Enhancers	Placenta	Placenta
16	chr6:39234200-39235000	Enhancers	Fetal Intestine Small	intestine
17	chr6:39234200-39235400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:39234600-39235000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr6:39234600-39236600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr6:39234600-39236800	Enhancers	H9 Cell Line	embryonic stem cell
21	chr6:39234600-39237000	Enhancers	Fetal Thymus	thymus
22	chr6:39234800-39235200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr6:39234800-39235400	Weak transcription	Thymus	Thymus
24	chr6:39234800-39237800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:39234800-39239000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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