Variant report

Variant	rs72854503
Chromosome Location	chr6:28248062-28248063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28248037-28248589	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr6:28248022-28248239	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27859121..27861068-chr6:28247840..28249566,2	K562	blood:
2	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
3	chr6:28193103..28195771-chr6:28247213..28248961,2	K562	blood:
4	chr6:28246460..28249146-chr6:28271252..28274232,2	K562	blood:
5	chr6:28247415..28251168-chr6:28301808..28306623,8	K562	blood:
6	chr6:28186460..28191177-chr6:28246836..28252039,7	K562	blood:
7	chr6:28191774..28193950-chr6:28248058..28250874,2	K562	blood:
8	chr6:28247781..28251138-chr6:28322226..28325499,4	K562	blood:

No data

Variant related genes	Relation type
PGBD1	TF binding region
ENSG00000233224	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000137185	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1150710	1.00[ASN][1000 genomes]
rs11546572	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2079705	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs41269285	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41269287	1.00[ASN][1000 genomes]
rs41269289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269291	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41270579	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs41270589	1.00[AFR][1000 genomes]
rs4540253	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61744109	1.00[ASN][1000 genomes]
rs62620226	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72844204	1.00[AFR][1000 genomes]
rs72844212	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72844218	1.00[AFR][1000 genomes]
rs72844220	1.00[AFR][1000 genomes]
rs72844226	1.00[AFR][1000 genomes]
rs72846777	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72846788	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72846792	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72846797	1.00[ASN][1000 genomes]
rs72846802	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849204	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849206	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849210	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849214	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849222	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72850297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850298	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72850299	1.00[AFR][1000 genomes]
rs72850300	1.00[AFR][1000 genomes]
rs72850302	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72851105	1.00[ASN][1000 genomes]
rs72851135	1.00[ASN][1000 genomes]
rs72851138	1.00[ASN][1000 genomes]
rs72851139	1.00[ASN][1000 genomes]
rs72851156	1.00[ASN][1000 genomes]
rs72851158	1.00[ASN][1000 genomes]
rs72851160	1.00[ASN][1000 genomes]
rs72851161	1.00[ASN][1000 genomes]
rs72851168	1.00[ASN][1000 genomes]
rs72851173	1.00[AFR][1000 genomes]
rs72851179	1.00[AFR][1000 genomes]
rs72851182	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72854506	1.00[ASN][1000 genomes]
rs72854515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854521	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72854522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854524	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72854525	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854527	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854531	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854533	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854535	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72854536	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72854542	0.85[AMR][1000 genomes]
rs72854546	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72854553	0.85[AMR][1000 genomes]
rs72854556	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7752415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28235400-28249000	Weak transcription	Small Intestine	intestine
2	chr6:28235600-28249000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:28235600-28249000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:28236200-28249400	Weak transcription	Fetal Heart	heart
5	chr6:28237400-28249000	Weak transcription	Psoas Muscle	Psoas
6	chr6:28237600-28248800	Weak transcription	A549	lung
7	chr6:28238000-28248800	Weak transcription	Hela-S3	cervix
8	chr6:28240600-28248600	Weak transcription	HMEC	breast
9	chr6:28240600-28249000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:28241000-28249000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:28241200-28249000	Weak transcription	Colonic Mucosa	Colon
12	chr6:28241800-28249000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:28242000-28249000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:28242200-28249200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:28242400-28249000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:28242600-28249000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:28242600-28249000	Weak transcription	Fetal Intestine Small	intestine
18	chr6:28244400-28249400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:28244600-28249400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:28244800-28248400	Weak transcription	Dnd41	blood
21	chr6:28244800-28248600	Weak transcription	NHDF-Ad	bronchial
22	chr6:28244800-28248800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:28244800-28248800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:28244800-28248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:28244800-28248800	Weak transcription	NH-A	brain
26	chr6:28245000-28248200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:28245000-28248600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:28245000-28248800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:28245000-28248800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:28245000-28248800	Weak transcription	NHLF	lung
31	chr6:28245000-28249000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:28245000-28249000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:28245000-28249000	Weak transcription	Esophagus	oesophagus
34	chr6:28245000-28249000	Weak transcription	Fetal Kidney	kidney
35	chr6:28245000-28249000	Weak transcription	Gastric	stomach
36	chr6:28245000-28249000	Weak transcription	Pancreas	Pancrea
37	chr6:28245000-28249000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr6:28245000-28249000	Weak transcription	Thymus	Thymus
39	chr6:28245000-28249000	Weak transcription	NHEK	skin
40	chr6:28245000-28249400	Weak transcription	Spleen	Spleen
41	chr6:28245200-28248600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:28245200-28248600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:28245200-28248600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:28245200-28248600	Weak transcription	Adipose Nuclei	Adipose
45	chr6:28245200-28248600	Weak transcription	Brain Substantia Nigra	brain
46	chr6:28245200-28248600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr6:28245200-28248800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:28245200-28248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:28245200-28248800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr6:28245200-28248800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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