Variant report

Variant	rs12462400
Chromosome Location	chr19:37422043-37422044
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37417109..37418736-chr19:37419934..37422422,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10402227	0.81[ASN][1000 genomes]
rs10403877	0.81[ASN][1000 genomes]
rs10410788	0.81[ASN][1000 genomes]
rs10424415	0.85[ASN][1000 genomes]
rs10426229	0.81[ASN][1000 genomes]
rs1114318	0.85[ASN][1000 genomes]
rs12459546	0.81[ASN][1000 genomes]
rs12460098	1.00[AFR][1000 genomes]
rs12460802	1.00[AFR][1000 genomes]
rs12460821	1.00[AFR][1000 genomes]
rs12461501	1.00[AFR][1000 genomes]
rs12462151	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12462186	1.00[AFR][1000 genomes]
rs12462205	1.00[AFR][1000 genomes]
rs12462623	1.00[AFR][1000 genomes]
rs12462629	1.00[AFR][1000 genomes]
rs12463214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1521096	1.00[AFR][1000 genomes]
rs16960966	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs16989369	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17239026	1.00[AFR][1000 genomes]
rs17721244	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17842485	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2305266	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3213840	1.00[AFR][1000 genomes]
rs35374722	1.00[AFR][1000 genomes]
rs36023046	1.00[AFR][1000 genomes]
rs57904468	0.81[ASN][1000 genomes]
rs59122318	0.81[ASN][1000 genomes]
rs73625272	1.00[AFR][1000 genomes]
rs9304876	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv911651	chr19:37300554-37428465	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
16	nsv523848	chr19:37357289-37487632	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37408200-37436400	Weak transcription	Fetal Thymus	thymus
2	chr19:37408200-37440600	Weak transcription	Stomach Mucosa	stomach
3	chr19:37408400-37440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr19:37408600-37439600	Weak transcription	Fetal Heart	heart
5	chr19:37409000-37444800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:37409000-37447400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:37409600-37423600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:37410600-37427600	Weak transcription	NH-A	brain
9	chr19:37413600-37427600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:37413800-37427400	Weak transcription	Right Ventricle	heart
11	chr19:37413800-37427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:37413800-37427800	Weak transcription	HSMMtube	muscle
13	chr19:37413800-37428000	Weak transcription	HUVEC	blood vessel
14	chr19:37415800-37444600	ZNF genes & repeats	Liver	Liver
15	chr19:37416200-37427800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr19:37418000-37422200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:37418600-37427400	Weak transcription	HSMM	muscle
18	chr19:37419200-37426200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
19	chr19:37419400-37447400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:37419600-37422800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr19:37420200-37423600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:37420200-37423600	ZNF genes & repeats	Fetal Stomach	stomach
23	chr19:37420600-37422200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
24	chr19:37420600-37422400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
25	chr19:37420600-37423600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
26	chr19:37420600-37423600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:37420600-37423600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:37420600-37423800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr19:37420600-37443000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
30	chr19:37420600-37447400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr19:37420600-37447600	ZNF genes & repeats	Adipose Nuclei	Adipose
32	chr19:37420800-37423600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:37421000-37423600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:37421200-37423600	Strong transcription	Fetal Muscle Leg	muscle
35	chr19:37421400-37422200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
36	chr19:37421400-37422200	Strong transcription	Brain Hippocampus Middle	brain
37	chr19:37421400-37422800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:37421400-37423000	Strong transcription	Fetal Brain Male	brain
39	chr19:37421400-37423000	Strong transcription	Osteobl	bone
40	chr19:37421400-37423400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:37421400-37423600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:37421400-37424200	ZNF genes & repeats	Primary T cells from cord blood	blood
43	chr19:37421600-37422200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:37421600-37422200	ZNF genes & repeats	Rectal Smooth Muscle	rectum
45	chr19:37421600-37422400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
46	chr19:37421600-37422400	Strong transcription	Brain Substantia Nigra	brain
47	chr19:37421600-37422400	ZNF genes & repeats	Colon Smooth Muscle	Colon
48	chr19:37421600-37422600	Strong transcription	Brain Anterior Caudate	brain
49	chr19:37421600-37422600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr19:37421600-37422800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood

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