Variant report

Variant	rs12976826
Chromosome Location	chr19:19729194-19729195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19728090..19730297-chr19:19774010..19775598,2	K562	blood:
2	chr19:19727841..19730107-chr19:19763060..19764845,2	MCF-7	breast:
3	chr19:19651405..19654732-chr19:19727842..19732175,4	MCF-7	breast:
4	chr19:19728345..19731839-chr19:19736250..19740547,12	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PBX4-1	chr19:19728917-19730355	ucscGeneNc_uc010ech_1

Variant related genes	Relation type
ENSG00000105726	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000064547	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10403759	0.99[ASN][1000 genomes]
rs10411387	1.00[ASW][hapmap]
rs10426732	1.00[ASW][hapmap]
rs11878202	0.99[ASN][1000 genomes]
rs11879838	0.96[ASN][1000 genomes]
rs12971734	1.00[CEU][hapmap]
rs12974308	0.81[EUR][1000 genomes]
rs12976582	0.81[EUR][1000 genomes]
rs12982049	0.81[EUR][1000 genomes]
rs1433079	0.81[EUR][1000 genomes]
rs16994684	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16996174	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1968047	0.95[ASN][1000 genomes]
rs2033481	1.00[CEU][hapmap];0.95[GIH][hapmap]
rs2043293	0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2304129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34558847	0.81[EUR][1000 genomes]
rs34725331	0.97[ASN][1000 genomes]
rs35035906	0.81[EUR][1000 genomes]
rs35445661	0.81[EUR][1000 genomes]
rs35449009	0.81[EUR][1000 genomes]
rs35792080	0.81[EUR][1000 genomes]
rs3752152	0.81[EUR][1000 genomes]
rs4808974	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7252228	0.97[ASN][1000 genomes]
rs739461	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs74181147	0.81[EUR][1000 genomes]
rs74181148	0.81[EUR][1000 genomes]
rs74181149	0.81[EUR][1000 genomes]
rs74181150	0.81[EUR][1000 genomes]
rs74181151	0.81[EUR][1000 genomes]
rs8101679	1.00[ASN][1000 genomes]
rs8113682	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs880090	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19727000-19729200	Weak transcription	Psoas Muscle	Psoas
2	chr19:19727000-19730200	Weak transcription	HepG2	liver
3	chr19:19727800-19729200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr19:19727800-19729200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr19:19728200-19729200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr19:19728200-19729600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr19:19728200-19730600	Enhancers	Fetal Brain Male	brain
8	chr19:19728400-19729200	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr19:19728400-19729800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr19:19728400-19729800	Active TSS	NHDF-Ad	bronchial
11	chr19:19728400-19730000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:19728400-19730000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:19728400-19730200	Flanking Active TSS	Dnd41	blood
14	chr19:19728600-19729200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr19:19728600-19729200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:19728600-19729200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr19:19728600-19729200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr19:19728600-19729200	Active TSS	Colonic Mucosa	Colon
19	chr19:19728600-19729200	Active TSS	Gastric	stomach
20	chr19:19728600-19729400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:19728600-19729400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:19728600-19729400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:19728600-19729400	Flanking Active TSS	Fetal Thymus	thymus
24	chr19:19728600-19729400	Flanking Active TSS	Thymus	Thymus
25	chr19:19728600-19729800	Active TSS	Brain Germinal Matrix	brain
26	chr19:19728600-19730000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:19728600-19730000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:19728600-19730000	Active TSS	Rectal Smooth Muscle	rectum
29	chr19:19728600-19730400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
30	chr19:19728800-19729200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:19728800-19729200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:19728800-19729200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr19:19728800-19729200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr19:19728800-19729200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:19728800-19729200	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr19:19728800-19729200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr19:19728800-19729200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:19728800-19729200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr19:19728800-19729200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
40	chr19:19728800-19729400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr19:19728800-19729400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:19728800-19729400	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr19:19728800-19729400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:19728800-19729400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:19728800-19729400	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr19:19728800-19729400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
47	chr19:19728800-19729400	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr19:19728800-19729400	Flanking Active TSS	Ovary	ovary
49	chr19:19728800-19729600	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr19:19728800-19729600	Active TSS	NHEK	skin

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