Variant report

Variant	rs1950001
Chromosome Location	chr7:39125413-39125414
allele	A/C
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	MAX	chr7:39125225-39125640	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr7:39125010-39125691	H1-neurons	neurons:	n/a	n/a
3	JUND	chr7:39125151-39125538	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr7:39125380-39125585	Gliobla	brain:	n/a	n/a
5	SIN3A	chr7:39125233-39125689	H1-hESC	embryonic stem cell:	n/a	n/a
6	REST	chr7:39124858-39125903	H1-neurons	neurons:	n/a	n/a
7	KAP1	chr7:39125014-39125688	HEK293	kidney:	n/a	n/a
8	KAP1	chr7:39125121-39125695	U2OS	brain:	n/a	n/a
9	POLR2A	chr7:39125036-39125856	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr7:39125059-39125701	H1-neurons	neurons:	n/a	n/a
11	ZNF263	chr7:39124956-39125691	HEK293-T-REx	kidney:	n/a	chr7:39125416-39125437 chr7:39125378-39125399
12	MXI1	chr7:39125390-39125709	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
POU6F2	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10224345	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10234489	0.89[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235824	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10248402	1.00[ASN][1000 genomes]
rs10254999	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10269214	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277485	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10480173	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1229057	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1405987	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1525790	1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525796	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs1527951	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs1527953	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1527957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881131	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140910	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2893570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4294102	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4452709	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4499996	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4499997	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4507668	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4588755	1.00[ASN][1000 genomes]
rs4720310	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs4723826	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723830	1.00[ASN][1000 genomes]
rs6462893	1.00[CEU][hapmap]
rs6955794	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6971923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976988	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs702820	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73122445	1.00[ASN][1000 genomes]
rs73126431	1.00[ASN][1000 genomes]
rs73126469	1.00[ASN][1000 genomes]
rs7778249	1.00[ASN][1000 genomes]
rs7778299	1.00[ASN][1000 genomes]
rs7787883	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7794776	0.80[EUR][1000 genomes]
rs859513	1.00[ASN][1000 genomes]
rs859542	1.00[ASN][1000 genomes]
rs859545	1.00[ASN][1000 genomes]
rs859546	1.00[ASN][1000 genomes]
rs859549	1.00[CHB][hapmap]
rs859550	1.00[CHB][hapmap]
rs859551	1.00[CHB][hapmap]
rs859552	1.00[CHB][hapmap]
rs859553	1.00[CHB][hapmap]
rs9986786	1.00[ASN][1000 genomes]
rs9987012	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv887968	chr7:39123165-39198960	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39123800-39126600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr7:39124400-39125800	Active TSS	Brain Cingulate Gyrus	brain
3	chr7:39124600-39126000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr7:39124800-39125600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:39124800-39125600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr7:39124800-39126000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr7:39124800-39126400	Active TSS	Right Atrium	heart
8	chr7:39125000-39125600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:39125000-39125600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:39125000-39125600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:39125000-39125600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:39125000-39125600	Active TSS	Aorta	Aorta
13	chr7:39125000-39125600	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr7:39125000-39125600	Flanking Active TSS	Fetal Brain Male	brain
15	chr7:39125000-39125800	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr7:39125000-39126000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:39125200-39125600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:39125200-39125600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr7:39125200-39125600	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr7:39125200-39125600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
21	chr7:39125200-39125600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:39125200-39125600	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
23	chr7:39125200-39125600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:39125200-39125600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:39125200-39125600	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr7:39125200-39125600	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr7:39125200-39125600	Active TSS	Brain Substantia Nigra	brain
28	chr7:39125200-39125600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr7:39125200-39125600	Active TSS	Fetal Kidney	kidney
30	chr7:39125200-39125600	Bivalent/Poised TSS	Fetal Lung	lung
31	chr7:39125200-39125600	Active TSS	Fetal Muscle Trunk	muscle
32	chr7:39125200-39125600	Active TSS	Placenta	Placenta
33	chr7:39125200-39125600	Active TSS	Lung	lung
34	chr7:39125200-39125600	Flanking Active TSS	Psoas Muscle	Psoas
35	chr7:39125200-39125600	Active TSS	Right Ventricle	heart
36	chr7:39125200-39125600	Active TSS	Stomach Smooth Muscle	stomach
37	chr7:39125200-39125800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:39125200-39125800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:39125200-39125800	Active TSS	Left Ventricle	heart
40	chr7:39125400-39125600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr7:39125400-39125600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
42	chr7:39125400-39125600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr7:39125400-39125600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
44	chr7:39125400-39125600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:39125400-39125600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr7:39125400-39125600	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr7:39125400-39125600	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
48	chr7:39125400-39125600	Flanking Active TSS	Fetal Brain Female	brain
49	chr7:39125400-39125600	Active TSS	Fetal Heart	heart
50	chr7:39125400-39125600	Bivalent Enhancer	Fetal Intestine Large	intestine

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