Variant report

Variant	rs3852857
Chromosome Location	chr19:45373539-45373540
allele	C/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	chr19:45373427-45373709	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr19:45373426-45373705	K562	blood:	n/a	n/a
3	SPI1	chr19:45373077-45373756	HL-60	blood:	n/a	chr19:45373446-45373459 chr19:45373511-45373520 chr19:45373612-45373625
4	POLR2A	chr19:45373292-45373689	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr19:45373110-45373618	NB4	blood:	n/a	n/a
6	POLR2A	chr19:45373281-45373837	K562	blood:	n/a	n/a
7	POLR2A	chr19:45373514-45373668	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:45372961-45373753	A549	lung:	n/a	n/a
9	MAX	chr19:45373287-45373795	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr19:45373329-45373741	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr19:45373279-45373701	K562	blood:	n/a	n/a
12	MYC	chr19:45373363-45373649	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr19:45373382-45373734	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr19:45373214-45373662	HepG2	liver:	n/a	n/a
15	FOS	chr19:45373387-45373763	HUVEC	blood vessel:	n/a	chr19:45373533-45373544 chr19:45373534-45373544 chr19:45373535-45373543
16	POLR2A	chr19:45373246-45373638	HepG2	liver:	n/a	n/a
17	NFIC	chr19:45373233-45373918	SK-N-SH	brain:	n/a	n/a
18	MXI1	chr19:45372909-45373784	IMR90	lung:	n/a	n/a
19	POLR2A	chr19:45373314-45373798	K562	blood:	n/a	n/a
20	MYC	chr19:45373188-45373635	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:45371836..45374441-chr19:45381288..45382864,3	MCF-7	breast:
2	chr19:45348165..45354069-chr19:45369473..45378418,11	MCF-7	breast:
3	chr19:45372550..45376273-chr19:45382475..45385600,3	K562	blood:

Variant related genes	Relation type
PVRL2	TF binding region
ENSG00000130202	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10424663	1.00[CHB][hapmap]
rs11667640	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11672399	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11879589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4081918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41290110	1.00[ASN][1000 genomes]
rs41290122	0.90[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	nsv534183	chr19:45351707-45385809	Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3852857	CTB-129P6.4	cis	Whole Blood	GTEx
rs3852857	PVRL2	cis	Whole Blood	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45352200-45375000	Weak transcription	HMEC	breast
2	chr19:45352600-45376200	Weak transcription	Brain Anterior Caudate	brain
3	chr19:45353000-45375200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr19:45353000-45375400	Weak transcription	NHDF-Ad	bronchial
5	chr19:45353000-45376000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:45354200-45375200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:45354200-45382600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:45355200-45375600	Weak transcription	Fetal Heart	heart
9	chr19:45357200-45375600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:45360400-45381800	Weak transcription	Psoas Muscle	Psoas
11	chr19:45361600-45377000	Weak transcription	Small Intestine	intestine
12	chr19:45363600-45374800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:45363600-45375000	Weak transcription	Fetal Lung	lung
14	chr19:45363600-45375200	Weak transcription	K562	blood
15	chr19:45365200-45375400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr19:45367200-45378800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:45367200-45392200	Strong transcription	Fetal Stomach	stomach
18	chr19:45367400-45382400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr19:45368000-45380400	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr19:45368000-45381200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr19:45368000-45383400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:45368200-45373800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr19:45368200-45379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:45368200-45379400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:45368200-45380000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:45368200-45382400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:45368200-45383400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:45368400-45373600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:45368600-45380400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:45368800-45375200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr19:45368800-45375400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:45369000-45374600	Weak transcription	Fetal Brain Female	brain
33	chr19:45369200-45374400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:45369400-45374400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr19:45369600-45375200	Genic enhancers	Fetal Intestine Small	intestine
36	chr19:45369800-45373800	Genic enhancers	Fetal Intestine Large	intestine
37	chr19:45369800-45393000	Weak transcription	Brain Angular Gyrus	brain
38	chr19:45370000-45377800	Weak transcription	Fetal Thymus	thymus
39	chr19:45370200-45375200	Weak transcription	Stomach Mucosa	stomach
40	chr19:45370400-45374600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr19:45371000-45373800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr19:45371000-45374200	Enhancers	HUVEC	blood vessel
43	chr19:45371200-45373800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr19:45371200-45373800	Enhancers	Placenta	Placenta
45	chr19:45371200-45374600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:45371200-45374600	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr19:45371200-45374800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr19:45371200-45375000	Weak transcription	Gastric	stomach
49	chr19:45371200-45375000	Weak transcription	Lung	lung
50	chr19:45371200-45375000	Weak transcription	Rectal Smooth Muscle	rectum

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