Variant report

Variant	rs28664038
Chromosome Location	chr19:19981955-19981956
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19975991..19979508-chr19:19981059..19984923,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF506-6	chr19:19981532-19982108	NONHSAT063610

Variant related genes	Relation type
ENSG00000256771	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10417812	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10419205	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10419574	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10421447	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28884245	0.84[EUR][1000 genomes]
rs58013871	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59284055	0.89[EUR][1000 genomes]
rs61692909	0.86[EUR][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

No data

Chromatin state (count:88 , 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	chr19:19978000-19982000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:19978000-19982600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:19978200-19993600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:19978400-19982000	Weak transcription	Gastric	stomach
8	chr19:19978400-19983200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr19:19978400-19984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:19978400-19984800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:19978400-19990800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:19978600-19982000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:19978600-19982000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:19978600-19982000	Weak transcription	Ovary	ovary
15	chr19:19978600-19982000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:19978600-19982000	Weak transcription	Thymus	Thymus
17	chr19:19978600-19982200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:19978600-19982200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:19978600-19982200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:19978600-19982400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr19:19978600-19983000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr19:19978600-19984800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:19978600-19984800	Weak transcription	Colonic Mucosa	Colon
24	chr19:19978600-19985000	Weak transcription	Placenta	Placenta
25	chr19:19978600-19989000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:19978600-19991000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr19:19978600-19992400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr19:19978600-19995200	Weak transcription	Pancreas	Pancrea
29	chr19:19978600-19996800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:19978600-19999000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:19978600-19999000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:19978600-19999000	Weak transcription	Right Ventricle	heart
33	chr19:19978800-19982000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:19978800-20007600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr19:19979000-20004000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr19:19979200-19982000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr19:19979200-19982000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr19:19979200-19982800	Weak transcription	Brain Anterior Caudate	brain
39	chr19:19979200-19982800	Weak transcription	K562	blood
40	chr19:19979200-19983200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr19:19979200-19985600	Weak transcription	Right Atrium	heart
42	chr19:19979200-19985800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:19979200-19988600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:19979200-20007400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:19979400-19982000	Weak transcription	Primary T cells from cord blood	blood
46	chr19:19979400-19982400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr19:19979400-19983600	Weak transcription	HepG2	liver
48	chr19:19979400-19990800	Weak transcription	Adipose Nuclei	Adipose
49	chr19:19979400-19996400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr19:19979400-19996800	Weak transcription	Brain Substantia Nigra	brain

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