Variant report

Variant	rs4768976
Chromosome Location	chr12:50830047-50830048
allele	C/T
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	POLR2A	chr12:50829648-50830106	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50829934..50834172-chr12:50845502..50848522,3	MCF-7	breast:

Variant related genes	Relation type
LARP4	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10467057	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10467107	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783361	1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876033	0.87[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10876035	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11169423	0.81[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17124559	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17124706	1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238105	1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4321029	0.82[EUR][1000 genomes]
rs4343103	1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4424740	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768936	1.00[JPT][hapmap]
rs57594106	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58723865	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138887	1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304630	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308184	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305121	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305168	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7489251	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959284	0.97[EUR][1000 genomes]
rs7964643	1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967393	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7970694	1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973910	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv899076	chr12:50770291-50869589	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
7	nsv469376	chr12:50792846-50856613	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
8	nsv558841	chr12:50792846-50856613	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
9	nsv470291	chr12:50792846-50858820	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50796800-50832600	Weak transcription	Brain Substantia Nigra	brain
2	chr12:50809600-50872200	Weak transcription	Fetal Brain Male	brain
3	chr12:50810600-50856600	Weak transcription	Aorta	Aorta
4	chr12:50815800-50834400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:50819200-50830200	Strong transcription	Fetal Stomach	stomach
6	chr12:50819200-50870800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:50819800-50842400	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:50819800-50867400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:50820000-50831600	Weak transcription	Psoas Muscle	Psoas
10	chr12:50820000-50835400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:50820000-50835600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:50820000-50841400	Weak transcription	Esophagus	oesophagus
13	chr12:50820000-50845400	Weak transcription	Right Atrium	heart
14	chr12:50820000-50867200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:50820200-50835200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:50820200-50869800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:50820200-50871000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:50820600-50839400	Strong transcription	Fetal Thymus	thymus
19	chr12:50820600-50843400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:50820800-50839600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:50821000-50839600	Strong transcription	Hela-S3	cervix
22	chr12:50821000-50841600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:50821000-50843000	Strong transcription	Placenta	Placenta
24	chr12:50821000-50850600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:50821200-50830200	Strong transcription	Fetal Muscle Leg	muscle
26	chr12:50821200-50845000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:50821200-50848200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr12:50821400-50845200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:50821600-50830200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:50821600-50830400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:50821600-50836200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:50821600-50836800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:50821600-50836800	Strong transcription	A549	lung
34	chr12:50821600-50839600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:50821600-50839600	Strong transcription	Adipose Nuclei	Adipose
36	chr12:50821600-50842800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:50821600-50850200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:50821600-50850200	Strong transcription	Fetal Intestine Large	intestine
39	chr12:50821600-50850600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr12:50821600-50850600	Strong transcription	Dnd41	blood
41	chr12:50821600-50850600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr12:50821600-50850800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:50821600-50851200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr12:50821600-50851600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:50821600-50851800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:50821600-50856800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:50821600-50863400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:50821600-50871400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:50821600-50872800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:50821800-50839600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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