Variant report

Variant	rs3851992
Chromosome Location	chr3:156399180-156399181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156398277..156399955-chr3:156533630..156535549,2	MCF-7	breast:
2	chr3:156398881..156401137-chr3:156542792..156545641,2	MCF-7	breast:
3	chr3:156391507..156394071-chr3:156396999..156400389,4	MCF-7	breast:
4	chr3:156398799..156400378-chr3:156543351..156545988,2	MCF-7	breast:
5	chr3:156397478..156399872-chr3:156533478..156536173,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243926	Chromatin interaction
ENSG00000240875	Chromatin interaction
ENSG00000197980	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10428096	0.85[AFR][1000 genomes]
rs10454220	0.84[AFR][1000 genomes]
rs11709829	0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12107178	0.80[AMR][1000 genomes]
rs13061457	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13068223	0.83[CHB][hapmap];0.95[GIH][hapmap]
rs1469536	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1560414	0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs34277251	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs345985	0.88[CHB][hapmap]
rs4098	0.84[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs66538320	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7638625	0.84[ASW][hapmap]
rs9818684	0.83[CHD][hapmap]
rs9818780	0.80[AFR][1000 genomes]
rs9867857	0.80[AFR][1000 genomes]
rs9878566	0.80[AFR][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	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3851992	VEPH1	cis	cerebellum	SCAN
rs3851992	TIPARP-AS1	cis	Thyroid	GTEx
rs3851992	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156393600-156401800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
2	chr3:156394000-156436000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:156394200-156412600	Weak transcription	Placenta	Placenta
4	chr3:156394400-156404800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:156394400-156411800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:156394600-156402200	Enhancers	Fetal Heart	heart
7	chr3:156394600-156402800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:156394800-156400600	Genic enhancers	K562	blood
9	chr3:156394800-156403000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:156395000-156400800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:156395400-156399200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:156395400-156400000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:156395400-156400000	Genic enhancers	Liver	Liver
14	chr3:156395400-156401400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:156395400-156402800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
16	chr3:156395600-156399200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:156395600-156399800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:156395600-156399800	Strong transcription	Fetal Thymus	thymus
19	chr3:156395600-156400000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:156395600-156401800	Genic enhancers	HUVEC	blood vessel
21	chr3:156395600-156438600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:156395800-156400200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:156395800-156400800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:156395800-156408600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:156396200-156399800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:156396200-156403600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:156396200-156407400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:156396400-156399600	Genic enhancers	Hela-S3	cervix
29	chr3:156396400-156407400	Weak transcription	Esophagus	oesophagus
30	chr3:156396400-156407400	Weak transcription	Spleen	Spleen
31	chr3:156396400-156408800	Weak transcription	Colonic Mucosa	Colon
32	chr3:156396400-156413000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:156396400-156414400	Weak transcription	Thymus	Thymus
34	chr3:156396400-156424800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:156396600-156400600	Enhancers	Brain Angular Gyrus	brain
36	chr3:156396600-156441000	Weak transcription	Lung	lung
37	chr3:156396800-156399200	Genic enhancers	NHLF	lung
38	chr3:156397200-156399200	Transcr. at gene 5' and 3'	Osteobl	bone
39	chr3:156397200-156399800	Transcr. at gene 5' and 3'	NHEK	skin
40	chr3:156397200-156400000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
41	chr3:156397200-156400200	Genic enhancers	Primary T cells from cord blood	blood
42	chr3:156397200-156400600	Enhancers	Fetal Intestine Small	intestine
43	chr3:156397200-156400600	Enhancers	Stomach Mucosa	stomach
44	chr3:156397400-156399200	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr3:156397400-156399800	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr3:156397600-156399200	Genic enhancers	NHDF-Ad	bronchial
47	chr3:156397600-156399400	Enhancers	Psoas Muscle	Psoas
48	chr3:156397600-156399600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:156397600-156399800	Genic enhancers	Primary B cells from cord blood	blood
50	chr3:156397600-156400000	Enhancers	Sigmoid Colon	Sigmoid Colon

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