Variant report

Variant	rs16975816
Chromosome Location	chr19:42970805-42970806
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	chr19:42968131..42971103-chr19:42973928..42976779,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10518265	1.00[EUR][1000 genomes]
rs16975748	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975813	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975848	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975958	1.00[EUR][1000 genomes]
rs1903724	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34044249	1.00[EUR][1000 genomes]
rs34097578	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34147019	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34366776	1.00[EUR][1000 genomes]
rs34381435	1.00[EUR][1000 genomes]
rs34637823	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34734442	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34760209	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34923099	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35002034	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35038065	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35135831	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35213872	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35266309	1.00[EUR][1000 genomes]
rs35312827	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35349390	1.00[EUR][1000 genomes]
rs35409716	0.89[AMR][1000 genomes]
rs35544765	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35855384	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35917849	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35969273	1.00[EUR][1000 genomes]
rs3745238	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4635443	1.00[EUR][1000 genomes]
rs55697425	1.00[EUR][1000 genomes]
rs56271304	1.00[EUR][1000 genomes]
rs56312460	1.00[EUR][1000 genomes]
rs57516100	1.00[EUR][1000 genomes]
rs58405647	1.00[EUR][1000 genomes]
rs58845793	1.00[EUR][1000 genomes]
rs59983776	1.00[EUR][1000 genomes]
rs60389892	1.00[EUR][1000 genomes]
rs60993923	1.00[EUR][1000 genomes]
rs61661961	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7253354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73932713	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73932727	1.00[EUR][1000 genomes]
rs73932730	1.00[EUR][1000 genomes]
rs73932732	1.00[EUR][1000 genomes]
rs73932734	1.00[EUR][1000 genomes]
rs73932736	1.00[EUR][1000 genomes]
rs73932737	1.00[EUR][1000 genomes]
rs73932738	1.00[EUR][1000 genomes]
rs73932739	1.00[EUR][1000 genomes]
rs73932741	1.00[EUR][1000 genomes]
rs73932742	1.00[EUR][1000 genomes]
rs73932744	1.00[EUR][1000 genomes]
rs73932746	1.00[EUR][1000 genomes]
rs73932747	1.00[EUR][1000 genomes]
rs73932748	1.00[EUR][1000 genomes]
rs73932750	1.00[EUR][1000 genomes]
rs73932751	1.00[EUR][1000 genomes]
rs73932752	1.00[EUR][1000 genomes]
rs73932754	1.00[EUR][1000 genomes]
rs73932761	1.00[EUR][1000 genomes]
rs73932762	1.00[EUR][1000 genomes]
rs73936020	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936024	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936031	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936032	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8105476	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109269	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs8110316	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	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42960200-42975600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:42960400-42971000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:42960400-42974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr19:42965800-42972400	Enhancers	Primary B cells from peripheral blood	blood
5	chr19:42967200-42972400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr19:42967200-42972400	Weak transcription	Esophagus	oesophagus
7	chr19:42967400-42972400	Weak transcription	Fetal Intestine Small	intestine
8	chr19:42969000-42972200	Enhancers	Primary B cells from cord blood	blood
9	chr19:42969200-42971000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:42969400-42971400	Flanking Active TSS	GM12878-XiMat	blood
11	chr19:42969400-42972000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr19:42969400-42973000	Enhancers	HepG2	liver
13	chr19:42969400-42975200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr19:42969800-42971400	Enhancers	Duodenum Mucosa	Duodenum
15	chr19:42969800-42971800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr19:42970000-42971000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:42970000-42971000	Enhancers	Left Ventricle	heart
18	chr19:42970000-42971600	Enhancers	Brain Cingulate Gyrus	brain
19	chr19:42970000-42971600	Enhancers	Lung	lung
20	chr19:42970000-42971600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr19:42970000-42971800	Enhancers	Adipose Nuclei	Adipose
22	chr19:42970000-42972600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:42970000-42972600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr19:42970000-42972600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:42970000-42974600	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr19:42970200-42971000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:42970200-42971000	Enhancers	Colonic Mucosa	Colon
28	chr19:42970200-42971000	Enhancers	Fetal Stomach	stomach
29	chr19:42970200-42971000	Enhancers	Right Atrium	heart
30	chr19:42970200-42971000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr19:42970200-42971200	Enhancers	Brain Anterior Caudate	brain
32	chr19:42970200-42971200	Enhancers	Placenta	Placenta
33	chr19:42970200-42971400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:42970200-42971600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:42970200-42971600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr19:42970200-42971600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr19:42970200-42971600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:42970200-42971600	Enhancers	Brain Hippocampus Middle	brain
39	chr19:42970200-42971600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr19:42970200-42971600	Enhancers	Spleen	Spleen
41	chr19:42970200-42971800	Enhancers	Brain Angular Gyrus	brain
42	chr19:42970200-42971800	Enhancers	Brain Substantia Nigra	brain
43	chr19:42970200-42972000	Enhancers	Primary hematopoietic stem cells	blood
44	chr19:42970200-42972600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:42970200-42972600	Enhancers	Muscle Satellite Cultured Cells	--
46	chr19:42970200-42972600	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr19:42970200-42972800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr19:42970200-42972800	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr19:42970400-42971200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr19:42970400-42971200	Enhancers	HUES48 Cell Line	embryonic stem cell

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