Variant report

Variant	rs1476459
Chromosome Location	chr19:19720028-19720029
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19717080..19720260-chr19:19736721..19739619,3	MCF-7	breast:
2	chr19:19707413..19710256-chr19:19720024..19721956,2	K562	blood:
3	chr19:19719609..19724823-chr19:19726829..19732010,6	MCF-7	breast:
4	chr19:19718034..19720062-chr19:19723408..19725424,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105717	Chromatin interaction
ENSG00000064547	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12611058	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12974028	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12977917	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12981270	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12982628	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12985142	0.84[EUR][1000 genomes]
rs33982830	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34096655	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34316070	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34316527	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34324119	0.86[EUR][1000 genomes]
rs34424437	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35209041	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35437712	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35553578	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35842591	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56083851	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62134460	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62137783	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62137816	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62137820	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62137822	0.98[EUR][1000 genomes]
rs7247165	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73004920	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs750216	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19706600-19728200	Weak transcription	Fetal Brain Male	brain
2	chr19:19707600-19728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:19708800-19724400	Weak transcription	NHDF-Ad	bronchial
4	chr19:19712800-19724400	Weak transcription	Gastric	stomach
5	chr19:19713800-19728000	Weak transcription	Brain Germinal Matrix	brain
6	chr19:19714000-19728800	Weak transcription	Brain Anterior Caudate	brain
7	chr19:19714200-19724400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr19:19717200-19724400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:19717400-19721200	Weak transcription	Placenta	Placenta
10	chr19:19717400-19721400	Weak transcription	GM12878-XiMat	blood
11	chr19:19717400-19721600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:19717400-19724200	Weak transcription	Fetal Muscle Leg	muscle
13	chr19:19717400-19724200	Weak transcription	A549	lung
14	chr19:19717400-19728000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr19:19717400-19728200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:19717400-19728600	Weak transcription	Esophagus	oesophagus
17	chr19:19717600-19724200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:19717600-19724400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:19717600-19724400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr19:19717600-19724400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:19717600-19724600	Weak transcription	Thymus	Thymus
22	chr19:19717600-19724800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:19717600-19726600	Weak transcription	Dnd41	blood
24	chr19:19717800-19724200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:19718000-19723200	Weak transcription	Hela-S3	cervix
26	chr19:19718000-19728000	Weak transcription	Primary T cells from cord blood	blood
27	chr19:19718400-19724200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:19718400-19724400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr19:19718400-19724400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr19:19718600-19724400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:19718800-19724600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr19:19719200-19726400	Weak transcription	Fetal Lung	lung
33	chr19:19719400-19720400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:19719600-19720200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:19719600-19725200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:19719600-19729000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:19719800-19726600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:19719800-19728600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:19719800-19728600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:19719800-19728800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:19720000-19720800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr19:19720000-19724200	Weak transcription	Fetal Stomach	stomach
43	chr19:19720000-19724400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr19:19720000-19724400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:19720000-19724400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:19720000-19724400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:19720000-19724400	Weak transcription	HSMMtube	muscle
48	chr19:19720000-19724800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr19:19720000-19725200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:19720000-19726600	Weak transcription	Fetal Brain Female	brain

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