Variant report

Variant	rs16976959
Chromosome Location	chr19:44490362-44490363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44486769..44491037-chr19:44505585..44508395,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159882	Chromatin interaction
ENSG00000266921	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10451441	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs11667318	1.00[EUR][1000 genomes]
rs11672570	1.00[EUR][1000 genomes]
rs12327743	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976952	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16978634	1.00[EUR][1000 genomes]
rs35026751	1.00[EUR][1000 genomes]
rs369958	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs378598	1.00[EUR][1000 genomes]
rs385016	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs405676	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs419277	0.89[ASN][1000 genomes]
rs424147	1.00[EUR][1000 genomes]
rs430107	1.00[EUR][1000 genomes]
rs439676	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs448921	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4599026	1.00[EUR][1000 genomes]
rs462723	0.89[ASN][1000 genomes]
rs57574350	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58379185	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59021410	0.89[ASN][1000 genomes]
rs59955744	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60213673	0.89[ASN][1000 genomes]
rs61254478	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650752	0.89[ASN][1000 genomes]
rs7260087	1.00[EUR][1000 genomes]
rs73567684	0.89[ASN][1000 genomes]
rs73567686	0.89[ASN][1000 genomes]
rs73567700	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73569807	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73569826	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73569841	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110949	1.00[EUR][1000 genomes]
rs8112679	1.00[EUR][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	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv912109	chr19:44459074-44493142	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44489000-44493600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:44489200-44490400	Enhancers	Fetal Heart	heart
3	chr19:44489200-44491600	Weak transcription	Aorta	Aorta
4	chr19:44489200-44492400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:44489200-44492400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr19:44489200-44492600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:44489200-44492600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:44489200-44492600	Weak transcription	Fetal Muscle Leg	muscle
9	chr19:44489200-44492600	Weak transcription	Psoas Muscle	Psoas
10	chr19:44489200-44493000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr19:44489200-44493200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:44489200-44493200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:44489200-44493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:44489200-44493400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:44489200-44493400	Weak transcription	Brain Angular Gyrus	brain
16	chr19:44489200-44493400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:44489200-44493600	Weak transcription	Colonic Mucosa	Colon
18	chr19:44489200-44494600	Weak transcription	Gastric	stomach
19	chr19:44489200-44494600	Weak transcription	NHLF	lung
20	chr19:44489200-44496000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:44489200-44496000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:44489200-44496000	Weak transcription	Small Intestine	intestine
23	chr19:44489200-44496600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr19:44489200-44500400	Weak transcription	HUVEC	blood vessel
25	chr19:44489200-44506200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr19:44489200-44506200	Weak transcription	Hela-S3	cervix
27	chr19:44489400-44491000	Weak transcription	Fetal Lung	lung
28	chr19:44489400-44491800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:44489400-44492000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:44489400-44492000	Weak transcription	Colon Smooth Muscle	Colon
31	chr19:44489400-44492200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr19:44489400-44492400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:44489400-44492400	Weak transcription	Pancreas	Pancrea
34	chr19:44489400-44492400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:44489400-44492400	Weak transcription	HSMM	muscle
36	chr19:44489400-44492600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:44489400-44492600	Weak transcription	Brain Germinal Matrix	brain
38	chr19:44489400-44492600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr19:44489400-44492600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr19:44489400-44492600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr19:44489400-44492600	Weak transcription	Thymus	Thymus
42	chr19:44489400-44492800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr19:44489400-44492800	Weak transcription	Brain Substantia Nigra	brain
44	chr19:44489400-44492800	Weak transcription	Fetal Brain Female	brain
45	chr19:44489400-44492800	Weak transcription	Fetal Thymus	thymus
46	chr19:44489400-44492800	Weak transcription	NHDF-Ad	bronchial
47	chr19:44489400-44493000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:44489400-44493200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:44489400-44493200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:44489400-44493200	Weak transcription	Placenta	Placenta

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