Variant report

Variant	rs16979230
Chromosome Location	chr19:38515280-38515281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38508262..38510811-chr19:38514830..38516559,2	K562	blood:
2	chr19:38514808..38516815-chr19:38528383..38531251,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1546800	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs17309382	0.83[ASN][1000 genomes]
rs57844882	0.92[EUR][1000 genomes]
rs61657018	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62121389	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62121390	0.91[EUR][1000 genomes]
rs62121391	0.91[EUR][1000 genomes]
rs62121392	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62121394	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS 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 target site	58 gene(s)	inside rSNPs	diseases
2	nsv911656	chr19:38505037-38539988	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1060359	chr19:38512719-38552438	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16979230	HNRNPUL1	cis	parietal	SCAN
rs16979230	PPP1R13L	cis	parietal	SCAN
rs16979230	ZNF780B	cis	parietal	SCAN
rs16979230	PHLDB3	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38495400-38522800	Weak transcription	Aorta	Aorta
2	chr19:38495400-38526400	Weak transcription	Ovary	ovary
3	chr19:38496200-38521400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:38496400-38521400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:38496600-38515600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr19:38496800-38520600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:38497400-38515800	Weak transcription	Fetal Brain Male	brain
8	chr19:38497400-38520600	Weak transcription	Primary T cells from cord blood	blood
9	chr19:38500600-38524200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr19:38501000-38521400	Weak transcription	Thymus	Thymus
11	chr19:38502400-38523000	Weak transcription	Liver	Liver
12	chr19:38503800-38523800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:38505200-38518600	Weak transcription	Fetal Stomach	stomach
14	chr19:38506200-38515600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:38506600-38526200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:38507400-38517800	Weak transcription	GM12878-XiMat	blood
17	chr19:38508000-38517000	Enhancers	Primary hematopoietic stem cells	blood
18	chr19:38508600-38537000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:38510000-38519600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:38510000-38524200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:38511400-38517400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr19:38512200-38521600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:38512600-38517400	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr19:38513200-38516600	Genic enhancers	Fetal Intestine Small	intestine
25	chr19:38513200-38517200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr19:38513200-38517200	Enhancers	Pancreas	Pancrea
27	chr19:38513400-38515800	Enhancers	Stomach Mucosa	stomach
28	chr19:38513400-38516200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:38513400-38516800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr19:38513400-38517200	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr19:38513600-38515400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr19:38513600-38515600	Enhancers	Fetal Kidney	kidney
33	chr19:38513600-38515800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:38513600-38515800	Genic enhancers	A549	lung
35	chr19:38513600-38516200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:38513600-38516200	Enhancers	Lung	lung
37	chr19:38513600-38516800	Enhancers	Fetal Muscle Trunk	muscle
38	chr19:38513600-38516800	Enhancers	NH-A	brain
39	chr19:38513600-38517200	Enhancers	Placenta	Placenta
40	chr19:38513600-38517400	Enhancers	Brain Hippocampus Middle	brain
41	chr19:38513800-38515800	Enhancers	Fetal Lung	lung
42	chr19:38513800-38524000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr19:38514000-38515800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:38514000-38520400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:38514000-38521400	Weak transcription	Esophagus	oesophagus
46	chr19:38514200-38515600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:38514200-38515600	Weak transcription	Spleen	Spleen
48	chr19:38514200-38516000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:38514200-38516600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:38514200-38516600	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links