Variant report

Variant	rs2384780
Chromosome Location	chr19:38708970-38708971
allele	C/T
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	CBX3	chr19:38708865-38709163	K562	blood:	n/a	n/a
2	CBX3	chr19:38708849-38709176	K562	blood:	n/a	n/a
3	RCOR1	chr19:38708940-38709100	Hela-S3	cervix:	n/a	n/a
4	RCOR1	chr19:38708924-38709243	K562	blood:	n/a	n/a
5	ZNF143	chr19:38708922-38709195	K562	blood:	n/a	n/a
6	RCOR1	chr19:38708866-38709218	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38704600..38706484-chr19:38706623..38709173,2	K562	blood:
2	chr19:38708386..38711062-chr19:38712686..38715377,3	K562	blood:

Variant related genes	Relation type
DPF1	TF binding region
ENSG00000011332	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12984978	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2255456	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304175	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304177	1.00[YRI][hapmap]
rs4802323	1.00[YRI][hapmap]
rs4802327	1.00[YRI][hapmap]
rs7256404	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[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	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2384780	B3GNT8	cis	cerebellum	SCAN
rs2384780	GIPR	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38685400-38713800	Weak transcription	HepG2	liver
2	chr19:38701400-38714600	Weak transcription	Right Atrium	heart
3	chr19:38701800-38713200	Weak transcription	NHEK	skin
4	chr19:38702600-38709200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:38702600-38713600	Weak transcription	Fetal Lung	lung
6	chr19:38702600-38714200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:38702600-38714400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:38702800-38709000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:38702800-38709000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr19:38702800-38712800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:38702800-38714200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:38702800-38714400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:38705000-38714400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:38705000-38714400	Weak transcription	Brain Substantia Nigra	brain
15	chr19:38705200-38712800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr19:38705400-38709000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:38705400-38709000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:38705400-38709000	Weak transcription	Brain Hippocampus Middle	brain
19	chr19:38705400-38713800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:38705400-38713800	Weak transcription	NHLF	lung
21	chr19:38705400-38714000	Weak transcription	NHDF-Ad	bronchial
22	chr19:38705400-38714200	Weak transcription	NH-A	brain
23	chr19:38706600-38713000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:38707000-38709000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:38707000-38709600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:38707000-38710400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:38707200-38710200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:38707200-38713200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:38707600-38714000	Weak transcription	Osteobl	bone
30	chr19:38707800-38713800	Weak transcription	Brain Angular Gyrus	brain
31	chr19:38707800-38713800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr19:38707800-38713800	Weak transcription	K562	blood
33	chr19:38707800-38714200	Weak transcription	HSMMtube	muscle
34	chr19:38708000-38710000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:38708000-38713000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:38708000-38713600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:38708000-38714000	Weak transcription	A549	lung
38	chr19:38708200-38713400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr19:38708400-38709600	Strong transcription	Fetal Muscle Leg	muscle
40	chr19:38708400-38709600	Strong transcription	Fetal Stomach	stomach
41	chr19:38708400-38711400	Weak transcription	Fetal Brain Male	brain
42	chr19:38708400-38713000	Strong transcription	Brain Germinal Matrix	brain
43	chr19:38708400-38713000	Strong transcription	Fetal Brain Female	brain
44	chr19:38708400-38713800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr19:38708400-38714000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:38708400-38714200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:38708600-38709800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:38708600-38710000	Strong transcription	Brain Anterior Caudate	brain
49	chr19:38708600-38710200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:38708600-38710200	Strong transcription	Fetal Muscle Trunk	muscle

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