Variant report

Variant	rs28362855
Chromosome Location	chr6:44234621-44234622
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr6:44233913-44234983	GM18505	blood:	n/a	n/a
2	NFIC	chr6:44233879-44234718	GM12878	blood:	n/a	n/a
3	MTA3	chr6:44229597-44234687	GM12878	blood:	n/a	n/a
4	RELA	chr6:44229670-44234939	GM12891	blood:	n/a	chr6:44230761-44230770 chr6:44230761-44230770 chr6:44231328-44231337 chr6:44231328-44231337
5	RUNX3	chr6:44233910-44234701	GM12878	blood:	n/a	n/a
6	TBL1XR1	chr6:44234054-44234637	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:44229152..44231602-chr6:44233591..44236343,2	MCF-7	breast:
2	chr6:44231911..44234847-chr6:44237510..44240187,2	MCF-7	breast:
3	chr6:44234120..44234767-chr6:44306292..44306910,2	MCF-7	breast:
4	chr6:44233082..44237547-chr6:44353791..44357282,5	MCF-7	breast:
5	chr6:44234588..44237594-chr6:44277478..44280850,3	MCF-7	breast:
6	chr6:44092343..44095710-chr6:44231665..44234902,4	K562	blood:
7	chr6:44231291..44234957-chr6:44353668..44356659,3	K562	blood:
8	chr6:44084290..44087287-chr6:44233720..44236514,2	K562	blood:
9	chr6:44233695..44236268-chr6:44306586..44308563,3	K562	blood:
10	chr6:44231603..44235224-chr6:44277267..44282023,5	MCF-7	breast:

No data

Variant related genes	Relation type
NFKBIE	TF binding region
TMEM151B	TF binding region
ENSG00000178233	Chromatin interaction
ENSG00000180992	Chromatin interaction
ENSG00000124608	Chromatin interaction
ENSG00000096401	Chromatin interaction
ENSG00000137216	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1044690	0.84[ASN][1000 genomes]
rs2233424	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233433	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2233434	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236500	0.94[EUR][1000 genomes]
rs28362854	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362859	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35623954	0.88[EUR][1000 genomes]
rs3734708	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3734709	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3799963	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41282670	0.88[EUR][1000 genomes]
rs60453984	0.85[EUR][1000 genomes]
rs61742784	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6458377	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
11	nsv885857	chr6:44223010-44250165	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44233000-44236000	Weak transcription	Fetal Heart	heart
2	chr6:44233400-44235800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:44233400-44235800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:44233400-44235800	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:44233400-44236000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:44233400-44236000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:44233400-44236200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:44233400-44236200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:44233400-44237000	Weak transcription	HMEC	breast
10	chr6:44233400-44237200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:44233400-44237400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:44233400-44237800	Weak transcription	Pancreas	Pancrea
13	chr6:44233400-44237800	Weak transcription	Right Ventricle	heart
14	chr6:44233600-44234800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr6:44233600-44234800	Flanking Active TSS	GM12878-XiMat	blood
16	chr6:44233600-44235400	Enhancers	K562	blood
17	chr6:44233600-44235600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:44233600-44235800	Weak transcription	Brain Anterior Caudate	brain
19	chr6:44233600-44235800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:44233600-44235800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:44233600-44236000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:44233600-44236000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:44233600-44236000	Weak transcription	Fetal Brain Male	brain
24	chr6:44233600-44236000	Weak transcription	Fetal Brain Female	brain
25	chr6:44233600-44236200	Weak transcription	Brain Substantia Nigra	brain
26	chr6:44233600-44238000	Weak transcription	Right Atrium	heart
27	chr6:44233800-44235400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:44233800-44236000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:44233800-44236000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:44233800-44236000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:44234000-44235200	Enhancers	Primary B cells from cord blood	blood
32	chr6:44234000-44235600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:44234000-44236000	Enhancers	Primary B cells from peripheral blood	blood
34	chr6:44234200-44235400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:44234600-44235600	Weak transcription	Fetal Thymus	thymus
36	chr6:44234600-44237200	Weak transcription	Spleen	Spleen

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