Variant report

Variant	rs28888982
Chromosome Location	chr19:19982719-19982720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19981310-19983337	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:19982711-19983030	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19975991..19979508-chr19:19981059..19984923,4	K562	blood:
2	chr19:19976277..19977796-chr19:19982374..19984542,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270270	TF binding region
ENSG00000256771	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10403255	0.81[AFR][1000 genomes]
rs10415179	0.89[AFR][1000 genomes]
rs10415754	0.82[EUR][1000 genomes]
rs10426937	0.81[AFR][1000 genomes]
rs2116888	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2304169	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7250258	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7254355	0.97[AFR][1000 genomes]
rs8105482	0.89[AFR][1000 genomes]
rs8113576	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking 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 miRNA	56 gene(s)	inside rSNPs	diseases
8	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	esv3413756	chr19:19936066-20072059	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv3380276	chr19:19936583-20073601	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1066792	chr19:19940585-20000701	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv3429980	chr19:19943721-20102072	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
14	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	53 gene(s)	inside rSNPs	diseases
15	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
16	nsv1057569	chr19:19973268-20193556	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28888982	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs28888982	ZNF682	cis	Muscle Skeletal	GTEx
rs28888982	ZNF93	cis	Muscle Skeletal	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19977600-19995600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:19977600-20006800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:19977800-19993200	Weak transcription	Spleen	Spleen
4	chr19:19978200-19993600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr19:19978400-19983200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr19:19978400-19984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:19978400-19984800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:19978400-19990800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:19978600-19983000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr19:19978600-19984800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:19978600-19984800	Weak transcription	Colonic Mucosa	Colon
12	chr19:19978600-19985000	Weak transcription	Placenta	Placenta
13	chr19:19978600-19989000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:19978600-19991000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:19978600-19992400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr19:19978600-19995200	Weak transcription	Pancreas	Pancrea
17	chr19:19978600-19996800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:19978600-19999000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:19978600-19999000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:19978600-19999000	Weak transcription	Right Ventricle	heart
21	chr19:19978800-20007600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:19979000-20004000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr19:19979200-19982800	Weak transcription	Brain Anterior Caudate	brain
24	chr19:19979200-19982800	Weak transcription	K562	blood
25	chr19:19979200-19983200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr19:19979200-19985600	Weak transcription	Right Atrium	heart
27	chr19:19979200-19985800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:19979200-19988600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:19979200-20007400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:19979400-19983600	Weak transcription	HepG2	liver
31	chr19:19979400-19990800	Weak transcription	Adipose Nuclei	Adipose
32	chr19:19979400-19996400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr19:19979400-19996800	Weak transcription	Brain Substantia Nigra	brain
34	chr19:19979400-20008200	ZNF genes & repeats	Liver	Liver
35	chr19:19979600-19984800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr19:19979600-19990800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:19979600-19991200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr19:19979600-19992800	Weak transcription	Brain Angular Gyrus	brain
39	chr19:19979600-19992800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:19979600-19996800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr19:19979800-19985800	Weak transcription	Fetal Lung	lung
42	chr19:19980000-19986800	Weak transcription	Colon Smooth Muscle	Colon
43	chr19:19980000-19987600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
44	chr19:19980000-19991200	Weak transcription	Brain Hippocampus Middle	brain
45	chr19:19980200-19983200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:19980200-19990800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:19980200-20001000	Weak transcription	Fetal Heart	heart
48	chr19:19980800-19983200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr19:19981000-19983200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr19:19981000-19983200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum

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