Variant report

Variant	rs2116939
Chromosome Location	chr19:44332497-44332498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44331547..44333384-chr19:45002930..45004694,2	MCF-7	breast:
2	chr19:44330249..44332710-chr19:44437495..44440338,2	MCF-7	breast:
3	chr19:44323198..44325701-chr19:44330167..44332994,2	K562	blood:

Variant related genes	Relation type
ENSG00000124459	Chromatin interaction
ENSG00000159871	Chromatin interaction
ENSG00000167384	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1061768	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16976835	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803661	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55727855	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55945626	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56098413	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56280239	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7248524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73050555	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73052643	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73052655	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73052663	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7508605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8103162	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2116939	SIGLEC16	cis	parietal	SCAN
rs2116939	CCDC8	cis	parietal	SCAN
rs2116939	SCAF1	cis	cerebellum	SCAN
rs2116939	KCNN4	cis	multi-tissue	Pritchard
rs2116939	ZNF615	cis	parietal	SCAN
rs2116939	LYPD5	cis	brain	seeQTL
rs2116939	PRKD2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44331000-44332600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:44331200-44332600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr19:44331200-44332600	Active TSS	HMEC	breast
4	chr19:44331200-44332800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:44332000-44332600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:44332000-44332600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr19:44332000-44332600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:44332000-44332800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:44332000-44334200	Weak transcription	Aorta	Aorta
10	chr19:44332000-44336800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:44332000-44339200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:44332000-44344400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:44332200-44332800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:44332200-44332800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:44332200-44332800	Weak transcription	Brain Substantia Nigra	brain
16	chr19:44332200-44332800	Weak transcription	Fetal Intestine Large	intestine
17	chr19:44332200-44332800	Weak transcription	Ovary	ovary
18	chr19:44332200-44333000	Weak transcription	Primary T cells from cord blood	blood
19	chr19:44332200-44333000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr19:44332200-44333000	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr19:44332200-44333000	Enhancers	Lung	lung
22	chr19:44332200-44333600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:44332200-44333800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:44332200-44334000	Weak transcription	Gastric	stomach
25	chr19:44332200-44334000	Weak transcription	Spleen	Spleen
26	chr19:44332200-44334200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr19:44332200-44334200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:44332200-44334200	Weak transcription	Pancreas	Pancrea
29	chr19:44332200-44334200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr19:44332200-44334200	Weak transcription	Thymus	Thymus
31	chr19:44332200-44334400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr19:44332200-44335400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:44332200-44335400	Weak transcription	Left Ventricle	heart
34	chr19:44332200-44336600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:44332200-44336800	Weak transcription	Esophagus	oesophagus
36	chr19:44332200-44338400	ZNF genes & repeats	A549	lung
37	chr19:44332200-44340400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr19:44332200-44341000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:44332400-44332600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:44332400-44332600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr19:44332400-44332600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
42	chr19:44332400-44332600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:44332400-44332600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr19:44332400-44332600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
45	chr19:44332400-44332600	Enhancers	Muscle Satellite Cultured Cells	--
46	chr19:44332400-44332600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
47	chr19:44332400-44332600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:44332400-44332600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:44332400-44332600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:44332400-44332600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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