Variant report

Variant	rs1864539
Chromosome Location	chr2:10090572-10090573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:10089602-10092724	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:10090536-10090580	MCF-7	breast:	n/a	n/a
3	MAX	chr2:10089567-10092486	HepG2	liver:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:9768803..9771575-chr2:10089760..10091656,2	MCF-7	breast:
2	chr2:10090078..10091613-chr2:10169348..10171878,2	K562	blood:
3	chr2:9982271..9986804-chr2:10090021..10093067,7	K562	blood:
4	chr2:9770089..9772474-chr2:10090151..10092445,2	K562	blood:
5	chr2:10089749..10091694-chr2:10096424..10099200,2	K562	blood:
6	chr2:9982092..9985559-chr2:10088577..10093200,6	MCF-7	breast:
7	chr2:9962243..9964669-chr2:10088779..10091216,2	MCF-7	breast:
8	chr2:10080626..10083275-chr2:10089838..10091585,2	K562	blood:
9	chr2:10090511..10093177-chr2:10182491..10184266,3	MCF-7	breast:
10	chr2:9982271..9985181-chr2:10090033..10093358,4	K562	blood:
11	chr2:10090081..10091760-chr2:10195035..10197397,2	K562	blood:
12	chr2:10090160..10094173-chr2:10181224..10185885,6	MCF-7	breast:
13	chr2:10085922..10087593-chr2:10089321..10091253,3	K562	blood:

No data

Variant related genes	Relation type
GRHL1	TF binding region
ENSG00000134308	Chromatin interaction
ENSG00000172059	Chromatin interaction
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1864540	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864541	0.85[JPT][hapmap]
rs1864542	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762536	0.87[MEX][hapmap]
rs3762539	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828260	0.83[MEX][hapmap]
rs891500	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv3409366	chr2:10090126-10092874	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	esv3369173	chr2:10090451-10093249	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10082000-10090800	Weak transcription	HMEC	breast
2	chr2:10085800-10090600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:10086000-10090800	Weak transcription	Pancreas	Pancrea
4	chr2:10086200-10090800	Weak transcription	Right Atrium	heart
5	chr2:10088800-10090800	Enhancers	Spleen	Spleen
6	chr2:10089800-10090600	Enhancers	Hela-S3	cervix
7	chr2:10089800-10091000	Enhancers	Lung	lung
8	chr2:10090000-10090600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:10090000-10090600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:10090000-10090800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
11	chr2:10090000-10092800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:10090200-10090600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
13	chr2:10090200-10090800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:10090200-10090800	Enhancers	Placenta Amnion	Placenta Amnion
15	chr2:10090200-10091000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr2:10090200-10091000	Flanking Bivalent TSS/Enh	HepG2	liver
17	chr2:10090200-10092600	Active TSS	Gastric	stomach
18	chr2:10090400-10090600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr2:10090400-10090600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
20	chr2:10090400-10090600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
21	chr2:10090400-10090600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
22	chr2:10090400-10090600	Enhancers	Dnd41	blood
23	chr2:10090400-10090800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:10090400-10090800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:10090400-10090800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:10090400-10090800	Flanking Active TSS	Esophagus	oesophagus
27	chr2:10090400-10090800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr2:10090400-10090800	Enhancers	Right Ventricle	heart
29	chr2:10090400-10091000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
30	chr2:10090400-10091200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:10090400-10091200	Flanking Active TSS	Placenta	Placenta
32	chr2:10090400-10091200	Bivalent Enhancer	Stomach Mucosa	stomach
33	chr2:10090400-10091400	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr2:10090400-10093000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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