Variant report

Variant	rs12982049
Chromosome Location	chr19:19780209-19780210
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19779650..19782100-chr19:19976513..19978467,2	MCF-7	breast:
2	chr19:19779787..19782276-chr19:19989567..19991864,2	K562	blood:
3	chr19:19779981..19782160-chr19:19842451..19845691,3	MCF-7	breast:
4	chr19:19779580..19781317-chr19:19788331..19791225,2	MCF-7	breast:
5	chr19:19772164..19776257-chr19:19777737..19781997,10	MCF-7	breast:
6	chr19:19779750..19782132-chr19:19785209..19787186,2	K562	blood:

Variant related genes	Relation type
ENSG00000105726	Chromatin interaction
ENSG00000256771	Chromatin interaction
ENSG00000105708	Chromatin interaction
ENSG00000181896	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]
rs12974308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
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	1.00[AFR][1000 genomes];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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74181148	1.00[AFR][1000 genomes];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	1.00[AFR][1000 genomes];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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19778200-19780400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr19:19778200-19781000	Active TSS	Primary T cells from cord blood	blood
3	chr19:19778800-19780400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:19778800-19780400	Active TSS	Rectal Smooth Muscle	rectum
5	chr19:19778800-19780600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr19:19778800-19780600	Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr19:19778800-19780600	Active TSS	Brain Hippocampus Middle	brain
8	chr19:19778800-19781400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr19:19778800-19781600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr19:19779000-19780400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:19779000-19780400	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr19:19779000-19780400	Active TSS	Muscle Satellite Cultured Cells	--
13	chr19:19779000-19780400	Active TSS	Lung	lung
14	chr19:19779000-19780400	Active TSS	HSMM	muscle
15	chr19:19779000-19780400	Active TSS	Osteobl	bone
16	chr19:19779000-19780600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:19779000-19780600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:19779000-19780600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:19779000-19780600	Active TSS	Fetal Kidney	kidney
20	chr19:19779000-19780600	Active TSS	Fetal Lung	lung
21	chr19:19779000-19780600	Active TSS	Right Atrium	heart
22	chr19:19779000-19780600	Active TSS	NHEK	skin
23	chr19:19779000-19780800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr19:19779000-19780800	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr19:19779000-19781000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:19779000-19781000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:19779000-19781000	Active TSS	Esophagus	oesophagus
28	chr19:19779000-19781000	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr19:19779000-19781200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:19779000-19781200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:19779000-19781400	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr19:19779200-19780400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:19779200-19780400	Active TSS	Brain Angular Gyrus	brain
34	chr19:19779200-19780400	Active TSS	Brain Cingulate Gyrus	brain
35	chr19:19779200-19780400	Active TSS	Thymus	Thymus
36	chr19:19779200-19780600	Active TSS	Left Ventricle	heart
37	chr19:19779200-19780800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:19779200-19780800	Active TSS	Fetal Intestine Small	intestine
39	chr19:19779200-19780800	Active TSS	HMEC	breast
40	chr19:19779200-19781000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:19779200-19781000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:19779200-19781200	Active TSS	Gastric	stomach
43	chr19:19779200-19781200	Active TSS	Small Intestine	intestine
44	chr19:19779400-19780400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:19779400-19780400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:19779400-19780400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:19779400-19780400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:19779400-19780400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:19779400-19780400	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr19:19779400-19780400	Active TSS	Primary T helper cells PMA-I stimulated	--

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