Variant report

Variant	rs859540
Chromosome Location	chr7:39015622-39015623
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr7:39015542-39016098	H1-hESC	embryonic stem cell:	n/a	chr7:39015896-39015906 chr7:39015691-39015703
2	EGR1	chr7:39015520-39015997	H1-hESC	embryonic stem cell:	n/a	chr7:39015751-39015764 chr7:39015803-39015814 chr7:39015751-39015764 chr7:39015753-39015763 chr7:39015751-39015764 chr7:39015752-39015763 chr7:39015747-39015769 chr7:39015895-39015908 chr7:39015754-39015763 chr7:39015751-39015765 chr7:39015754-39015764 chr7:39015666-39015676
3	GABPA	chr7:39015464-39015997	H1-hESC	embryonic stem cell:	n/a	chr7:39015669-39015678
4	YY1	chr7:39015580-39016216	H1-hESC	embryonic stem cell:	n/a	chr7:39015664-39015678
5	SIN3A	chr7:39015545-39016083	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr7:39015598-39016032	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr7:39015538-39016090	H1-hESC	embryonic stem cell:	n/a	chr7:39015896-39015906 chr7:39015691-39015703
8	CHD2	chr7:39015585-39015825	H1-hESC	embryonic stem cell:	n/a	chr7:39015794-39015804
9	EGR1	chr7:39015618-39015843	K562	blood:	n/a	chr7:39015751-39015764 chr7:39015803-39015814 chr7:39015751-39015764 chr7:39015753-39015763 chr7:39015751-39015764 chr7:39015752-39015763 chr7:39015747-39015769 chr7:39015754-39015763 chr7:39015751-39015765 chr7:39015754-39015764 chr7:39015666-39015676
10	CCNT2	chr7:39015611-39015783	K562	blood:	n/a	n/a
11	RAD21	chr7:39015472-39016163	H1-hESC	embryonic stem cell:	n/a	chr7:39015896-39015906 chr7:39015691-39015703
12	TBP	chr7:39015538-39016113	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
POU6F2	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1229009	1.00[ASN][1000 genomes]
rs1229026	1.00[ASN][1000 genomes]
rs1229029	1.00[ASN][1000 genomes]
rs1229051	1.00[ASN][1000 genomes]
rs59190975	1.00[ASN][1000 genomes]
rs859515	1.00[ASN][1000 genomes]
rs859516	1.00[ASN][1000 genomes]
rs859518	1.00[ASN][1000 genomes]
rs859531	1.00[ASN][1000 genomes]
rs859536	1.00[ASN][1000 genomes]
rs859539	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[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	nsv830967	chr7:38913837-39069253	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1024142	chr7:38978728-39300444	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv887967	chr7:39009307-39090698	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39014600-39015800	Enhancers	Fetal Brain Male	brain
2	chr7:39015200-39015800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
3	chr7:39015200-39015800	Active TSS	Stomach Smooth Muscle	stomach
4	chr7:39015200-39016000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:39015200-39016200	Active TSS	Fetal Brain Female	brain
6	chr7:39015200-39016400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr7:39015200-39021200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr7:39015400-39015800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:39015400-39015800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
10	chr7:39015400-39015800	Active TSS	Pancreas	Pancrea
11	chr7:39015400-39015800	Active TSS	Rectal Smooth Muscle	rectum
12	chr7:39015400-39015800	Bivalent Enhancer	Right Ventricle	heart
13	chr7:39015400-39016000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
14	chr7:39015400-39016000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr7:39015400-39016000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:39015400-39016000	Bivalent/Poised TSS	Right Atrium	heart
17	chr7:39015400-39016200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr7:39015400-39016200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:39015400-39016200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:39015400-39016200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
21	chr7:39015400-39016200	Active TSS	Aorta	Aorta
22	chr7:39015400-39016200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:39015400-39016400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr7:39015400-39016400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr7:39015400-39016400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr7:39015600-39015800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
27	chr7:39015600-39015800	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:39015600-39015800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:39015600-39015800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:39015600-39015800	Active TSS	Brain Angular Gyrus	brain
31	chr7:39015600-39015800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr7:39015600-39015800	Bivalent Enhancer	Esophagus	oesophagus
33	chr7:39015600-39015800	Bivalent/Poised TSS	Fetal Stomach	stomach
34	chr7:39015600-39015800	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion
35	chr7:39015600-39015800	Bivalent Enhancer	HMEC	breast
36	chr7:39015600-39016000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:39015600-39016000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:39015600-39016000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
39	chr7:39015600-39016000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
40	chr7:39015600-39016000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:39015600-39016000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:39015600-39016000	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr7:39015600-39016000	Flanking Active TSS	Liver	Liver
44	chr7:39015600-39016000	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr7:39015600-39016000	Bivalent/Poised TSS	Colonic Mucosa	Colon
46	chr7:39015600-39016000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
47	chr7:39015600-39016000	Flanking Bivalent TSS/Enh	Left Ventricle	heart
48	chr7:39015600-39016000	Bivalent/Poised TSS	Ovary	ovary
49	chr7:39015600-39016000	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
50	chr7:39015600-39016000	Bivalent/Poised TSS	NH-A	brain

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