Variant report

Variant	rs16863239
Chromosome Location	chr3:150904279-150904280
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	MYC	chr3:150904254-150904300	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
MED12L	TF binding region
RNA5SP145	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11707833	1.00[EUR][1000 genomes]
rs11713719	0.83[JPT][hapmap];1.00[EUR][1000 genomes]
rs11714357	0.82[JPT][hapmap]
rs11714651	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11715095	1.00[EUR][1000 genomes]
rs11715411	1.00[EUR][1000 genomes]
rs1355125	1.00[EUR][1000 genomes]
rs16863149	0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs16863153	0.83[JPT][hapmap];1.00[EUR][1000 genomes]
rs16863161	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs16863203	0.83[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16863204	1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16863227	0.91[JPT][hapmap]
rs16863238	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16863305	1.00[YRI][hapmap]
rs3732756	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732757	1.00[YRI][hapmap]
rs3821668	1.00[YRI][hapmap]
rs58593708	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs906766	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150872800-150910800	Weak transcription	Brain Germinal Matrix	brain
2	chr3:150873200-150910200	Weak transcription	Brain Angular Gyrus	brain
3	chr3:150873800-150913800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:150878000-150946000	Weak transcription	Placenta	Placenta
5	chr3:150884200-150906600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:150889200-150908200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:150889200-150914800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:150889600-150913800	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:150890600-150923400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:150896200-150927800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:150896400-150904400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:150896600-150918200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:150897200-150916200	Weak transcription	Fetal Intestine Small	intestine
14	chr3:150897600-150913800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:150898600-150917200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:150899000-150917000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:150900400-150910200	Weak transcription	Fetal Brain Female	brain
18	chr3:150900400-150917200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:150900600-150908400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:150900600-150917000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:150900800-150917200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:150901000-150908600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:150901200-150907000	Weak transcription	Thymus	Thymus
24	chr3:150901200-150917600	Weak transcription	Fetal Thymus	thymus
25	chr3:150901200-150917800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:150901400-150908400	Weak transcription	Dnd41	blood
27	chr3:150901400-150910200	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:150901400-150911600	Weak transcription	Brain Substantia Nigra	brain
29	chr3:150901400-150914200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:150901400-150916200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:150901600-150906800	Weak transcription	HepG2	liver
32	chr3:150901600-150913600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:150901800-150918000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:150902000-150906600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:150902200-150906600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:150902200-150916400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:150902400-150904400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr3:150902600-150904400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:150902600-150904600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:150903600-150904400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:150904000-150904800	Strong transcription	Brain Anterior Caudate	brain
42	chr3:150904000-150905000	Enhancers	Primary T cells from cord blood	blood
43	chr3:150904200-150904400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:150904200-150904400	ZNF genes & repeats	Aorta	Aorta
45	chr3:150904200-150904600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:150904200-150904600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:150904200-150904600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:150904200-150904800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr3:150904200-150911800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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