Variant report

Variant	rs10460316
Chromosome Location	chr2:153243926-153243927
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	EP300	chr2:153241991-153244319	SK-N-SH	brain:	n/a	chr2:153242638-153242652 chr2:153243952-153243960 chr2:153242319-153242329
2	GATA2	chr2:153243639-153244290	SH-SY5Y	brain:	n/a	chr2:153243692-153243708
3	EP300	chr2:153243689-153244012	SK-N-SH_RA	brain:	n/a	chr2:153243952-153243960
4	EP300	chr2:153243679-153244022	SK-N-SH_RA	brain:	n/a	chr2:153243952-153243960

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153237750..153240255-chr2:153243184..153245369,2	K562	blood:

Variant related genes	Relation type
ENSG00000213197	TF binding region

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11884490	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11897348	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12105483	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12468749	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12471256	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12986786	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16831031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831043	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16831135	0.81[EUR][1000 genomes]
rs16831229	0.83[EUR][1000 genomes]
rs2345875	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2881338	0.83[EUR][1000 genomes]
rs34027587	0.86[EUR][1000 genomes]
rs34424354	0.81[ASN][1000 genomes]
rs35455499	0.81[EUR][1000 genomes]
rs4233659	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4293523	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4664108	0.85[EUR][1000 genomes]
rs4664111	0.83[EUR][1000 genomes]
rs4664575	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4664584	0.83[EUR][1000 genomes]
rs4664588	0.83[EUR][1000 genomes]
rs60280470	0.88[EUR][1000 genomes]
rs7582905	0.81[EUR][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	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153207600-153246400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:153224800-153246000	Weak transcription	Fetal Stomach	stomach
3	chr2:153226200-153249400	Weak transcription	Right Ventricle	heart
4	chr2:153226200-153251800	Weak transcription	HSMMtube	muscle
5	chr2:153229200-153252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:153233400-153249000	Weak transcription	Gastric	stomach
7	chr2:153233600-153246200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:153233800-153245600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:153233800-153255400	Weak transcription	NHEK	skin
10	chr2:153237400-153246200	Weak transcription	Placenta	Placenta
11	chr2:153237400-153249000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:153237400-153255400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:153237400-153255400	Weak transcription	HMEC	breast
14	chr2:153238400-153246400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:153238600-153245600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:153238600-153246600	Weak transcription	Ovary	ovary
17	chr2:153238600-153258600	Weak transcription	Left Ventricle	heart
18	chr2:153240600-153244400	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr2:153240800-153244000	Enhancers	Brain Substantia Nigra	brain
20	chr2:153241200-153244200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:153241200-153245600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:153241200-153251600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:153241200-153255400	Weak transcription	Pancreas	Pancrea
24	chr2:153241600-153244000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr2:153241600-153249000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:153242200-153244600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:153242600-153245000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:153242600-153245000	Weak transcription	Brain Angular Gyrus	brain
29	chr2:153242600-153247200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:153242800-153245200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:153242800-153247800	Weak transcription	Psoas Muscle	Psoas
32	chr2:153242800-153248000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:153242800-153248000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:153242800-153249200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:153242800-153252600	Weak transcription	A549	lung
36	chr2:153243000-153245000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:153243000-153247200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:153243000-153251600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr2:153243200-153244400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:153243200-153249200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:153243400-153246000	Weak transcription	HepG2	liver
42	chr2:153243400-153247400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:153243400-153252600	Weak transcription	Fetal Brain Female	brain
44	chr2:153243600-153244400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:153243600-153244600	Weak transcription	Brain Hippocampus Middle	brain
46	chr2:153243600-153245000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:153243600-153247000	Weak transcription	Brain Anterior Caudate	brain
48	chr2:153243800-153245800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:153243800-153246800	Weak transcription	Stomach Mucosa	stomach
50	chr2:153243800-153252000	Weak transcription	Fetal Lung	lung

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