Variant report

Variant	rs28637729
Chromosome Location	chr19:39939551-39939552
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	chr19:39938346..39940025-chr19:39963736..39966601,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10423537	0.87[EUR][1000 genomes]
rs10424217	0.84[EUR][1000 genomes]
rs1130180	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12609112	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12978920	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12983040	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1529732	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1560730	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1865091	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1865092	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1932	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2009970	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2060270	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2060271	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2116932	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2288933	0.85[EUR][1000 genomes]
rs2288934	0.86[EUR][1000 genomes]
rs2304219	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2304221	0.87[EUR][1000 genomes]
rs2353678	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2353679	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs251855	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs251856	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs251857	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs251858	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs251859	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs251860	0.82[EUR][1000 genomes]
rs28528765	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28649498	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs31727	0.80[AMR][1000 genomes]
rs34918990	0.87[EUR][1000 genomes]
rs35647910	0.86[EUR][1000 genomes]
rs4390710	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4802026	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803237	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4803240	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803241	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4803242	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4803245	0.85[EUR][1000 genomes]
rs4803246	0.84[EUR][1000 genomes]
rs4803247	0.85[EUR][1000 genomes]
rs566130	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58884220	0.82[AFR][1000 genomes]
rs59007555	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6508862	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6508863	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6508864	0.85[EUR][1000 genomes]
rs6508865	0.82[EUR][1000 genomes]
rs686956	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7251384	0.84[EUR][1000 genomes]
rs7251652	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7255253	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73035416	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73549933	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8107194	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8107647	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8110134	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8110716	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8111260	0.84[EUR][1000 genomes]
rs878754	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
6	nsv544003	chr19:39937078-39974282	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28637729	RPS16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39936800-39949200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:39937000-39949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:39937000-39971000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:39937200-39940600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:39937200-39941600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:39937200-39943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:39937400-39940000	Genic enhancers	Brain Cingulate Gyrus	brain
8	chr19:39937400-39940200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:39937400-39941200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:39937400-39942800	Weak transcription	Fetal Kidney	kidney
11	chr19:39937400-39944600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:39937400-39971000	Weak transcription	Right Atrium	heart
13	chr19:39937600-39940000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr19:39937600-39940000	Enhancers	Liver	Liver
15	chr19:39937600-39940000	Genic enhancers	NHLF	lung
16	chr19:39937600-39940200	Genic enhancers	Brain Angular Gyrus	brain
17	chr19:39937600-39940200	Genic enhancers	K562	blood
18	chr19:39937600-39940400	Genic enhancers	Brain Germinal Matrix	brain
19	chr19:39937600-39946000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:39937600-39950000	Weak transcription	Fetal Brain Male	brain
21	chr19:39937800-39939600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:39937800-39940000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:39937800-39940200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:39937800-39940600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
25	chr19:39937800-39941600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr19:39937800-39942200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:39937800-39943400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:39937800-39946200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:39938000-39940000	Genic enhancers	Dnd41	blood
30	chr19:39938000-39941800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr19:39938000-39942200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr19:39938200-39940000	Genic enhancers	Primary T cells fromperipheralblood	blood
33	chr19:39938200-39940600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:39938200-39942800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:39938400-39939800	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr19:39938400-39940000	Enhancers	Small Intestine	intestine
37	chr19:39938400-39940200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:39938400-39940200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:39938400-39940400	Genic enhancers	Primary T cells from cord blood	blood
40	chr19:39938400-39940400	Genic enhancers	Adipose Nuclei	Adipose
41	chr19:39938400-39941400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr19:39938400-39941400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:39938600-39940000	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr19:39938600-39940000	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr19:39938600-39940000	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr19:39938600-39940200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
47	chr19:39938600-39940200	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr19:39938600-39940200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:39938600-39940200	Genic enhancers	Left Ventricle	heart
50	chr19:39938600-39940400	Genic enhancers	Pancreas	Pancrea

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