Variant report

Variant	rs12974308
Chromosome Location	chr19:19778155-19778156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19772164..19776257-chr19:19777737..19781997,10	MCF-7	breast:
2	chr19:19702026..19704512-chr19:19777801..19779336,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105726	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10402516	0.84[ASN][1000 genomes]
rs10405234	0.82[ASN][1000 genomes]
rs10423311	0.82[ASN][1000 genomes]
rs11667828	0.82[ASN][1000 genomes]
rs11670710	0.99[ASN][1000 genomes]
rs12976582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12976826	0.81[EUR][1000 genomes]
rs12980482	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12982049	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12982500	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12983292	0.99[ASN][1000 genomes]
rs1433079	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16994684	0.83[EUR][1000 genomes]
rs16996174	0.83[EUR][1000 genomes]
rs16996227	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288865	0.83[ASN][1000 genomes]
rs2288867	0.82[ASN][1000 genomes]
rs2304129	0.81[EUR][1000 genomes]
rs28472726	0.80[ASN][1000 genomes]
rs28635562	0.82[ASN][1000 genomes]
rs34558847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35035906	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35445661	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35449009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35792080	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35801717	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3752152	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3794996	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4808209	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808974	0.81[EUR][1000 genomes]
rs4808976	0.82[ASN][1000 genomes]
rs4808979	0.87[ASN][1000 genomes]
rs4808981	0.87[ASN][1000 genomes]
rs7247142	0.91[ASN][1000 genomes]
rs7249670	0.99[ASN][1000 genomes]
rs7251924	0.95[ASN][1000 genomes]
rs74181147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74181148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74181149	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74181150	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74181151	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv911310	chr19:19753882-19784891	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 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	chr19:19774200-19779000	Weak transcription	Fetal Heart	heart
2	chr19:19774800-19779000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr19:19775000-19778400	Weak transcription	Spleen	Spleen
4	chr19:19775200-19778200	Weak transcription	Liver	Liver
5	chr19:19775200-19778400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:19775200-19778400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr19:19775200-19778800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr19:19775200-19778800	Weak transcription	HUVEC	blood vessel
9	chr19:19775200-19779000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:19775200-19779000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr19:19775200-19779000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:19775200-19779000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:19775200-19779000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr19:19775200-19779000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:19775200-19779000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:19775200-19779000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr19:19775200-19779000	Weak transcription	Brain Angular Gyrus	brain
18	chr19:19775200-19779000	Weak transcription	Brain Anterior Caudate	brain
19	chr19:19775200-19779000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:19775200-19779000	Weak transcription	Brain Germinal Matrix	brain
21	chr19:19775200-19779000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:19775200-19779000	Weak transcription	Brain Substantia Nigra	brain
23	chr19:19775200-19779000	Weak transcription	Colonic Mucosa	Colon
24	chr19:19775200-19779000	Weak transcription	Colon Smooth Muscle	Colon
25	chr19:19775200-19779000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr19:19775200-19779000	Weak transcription	Fetal Brain Male	brain
27	chr19:19775200-19779000	Weak transcription	Fetal Brain Female	brain
28	chr19:19775200-19779000	Weak transcription	Fetal Stomach	stomach
29	chr19:19775200-19779000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:19775200-19779000	Weak transcription	Psoas Muscle	Psoas
31	chr19:19775200-19779000	Weak transcription	Right Ventricle	heart
32	chr19:19775200-19779000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr19:19775200-19779000	Weak transcription	HSMMtube	muscle
34	chr19:19775200-19779000	Weak transcription	NH-A	brain
35	chr19:19775200-19779000	Weak transcription	NHLF	lung
36	chr19:19775200-19779200	Weak transcription	Stomach Mucosa	stomach
37	chr19:19775200-19779200	Weak transcription	A549	lung
38	chr19:19775200-19779200	Weak transcription	NHDF-Ad	bronchial
39	chr19:19775400-19778200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr19:19775400-19778200	Weak transcription	Primary T cells from cord blood	blood
41	chr19:19775400-19778200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr19:19775400-19778400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr19:19775400-19778400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr19:19775400-19778400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr19:19775400-19778400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr19:19775400-19778400	Enhancers	Primary T cells fromperipheralblood	blood
47	chr19:19775400-19778800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr19:19775400-19778800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:19775400-19778800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:19775400-19779000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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