Variant report

Variant	rs236312
Chromosome Location	chr1:94088650-94088651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94085180..94089812-chr1:94310226..94315311,7	MCF-7	breast:
2	chr1:94088580..94091392-chr1:94145973..94148606,2	MCF-7	breast:
3	chr1:94076613..94078527-chr1:94088033..94090133,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260464	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000211575	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12084853	1.00[JPT][hapmap]
rs12568405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1618866	0.91[ASN][1000 genomes]
rs1740068	0.91[ASN][1000 genomes]
rs1772781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1772782	0.96[ASN][1000 genomes]
rs182913	0.88[ASN][1000 genomes]
rs183538	0.91[ASN][1000 genomes]
rs236266	1.00[JPT][hapmap]
rs236267	0.93[ASN][1000 genomes]
rs236270	0.91[ASN][1000 genomes]
rs236271	0.91[ASN][1000 genomes]
rs236273	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs236274	0.88[ASN][1000 genomes]
rs236275	0.88[ASN][1000 genomes]
rs236277	0.93[ASN][1000 genomes]
rs236278	0.88[ASN][1000 genomes]
rs236281	0.88[ASN][1000 genomes]
rs236285	0.80[AMR][1000 genomes]
rs236288	0.83[AMR][1000 genomes]
rs236291	0.85[AMR][1000 genomes]
rs236295	1.00[JPT][hapmap]
rs236296	1.00[JPT][hapmap]
rs236301	0.86[AMR][1000 genomes]
rs236306	1.00[CEU][hapmap];0.84[CHD][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs236307	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs236308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs236311	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs236313	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs236343	0.82[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs236344	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs236345	0.83[EUR][1000 genomes]
rs368888	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3767979	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs3767981	0.93[ASN][1000 genomes]
rs3767987	0.93[ASN][1000 genomes]
rs3767991	1.00[JPT][hapmap]
rs399649	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs423493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60159857	0.91[ASN][1000 genomes]
rs6541387	1.00[JPT][hapmap]
rs6702036	1.00[JPT][hapmap]
rs6704479	1.00[JPT][hapmap]
rs798213	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798217	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798218	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs236312	BCAR3	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:94077200-94099000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:94079600-94089400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:94079800-94090000	Enhancers	Stomach Mucosa	stomach
5	chr1:94080000-94089200	Genic enhancers	NHEK	skin
6	chr1:94081200-94095000	Genic enhancers	HSMM	muscle
7	chr1:94083400-94091200	Weak transcription	Aorta	Aorta
8	chr1:94083400-94093800	Weak transcription	Psoas Muscle	Psoas
9	chr1:94083400-94108200	Weak transcription	Esophagus	oesophagus
10	chr1:94083600-94101600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:94083800-94091200	Weak transcription	Ovary	ovary
12	chr1:94083800-94091400	Weak transcription	Fetal Stomach	stomach
13	chr1:94083800-94095000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:94084000-94089400	Genic enhancers	HMEC	breast
15	chr1:94084000-94089800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:94084000-94090800	Weak transcription	Fetal Lung	lung
17	chr1:94084000-94091000	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:94084000-94091400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:94084200-94090000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:94084200-94090800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:94084200-94091400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:94084200-94101000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:94084400-94091400	Enhancers	HepG2	liver
24	chr1:94084600-94091200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:94085200-94091000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:94085200-94091400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:94085200-94092200	Enhancers	Placenta	Placenta
28	chr1:94085400-94093600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:94085400-94107600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:94085800-94089200	Genic enhancers	Muscle Satellite Cultured Cells	--
31	chr1:94085800-94090400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:94085800-94091800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:94086200-94091600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:94086200-94092600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:94086400-94089000	Weak transcription	HSMMtube	muscle
36	chr1:94086800-94098000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:94086800-94101200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:94087000-94091200	Weak transcription	Small Intestine	intestine
39	chr1:94087200-94089600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:94087200-94091000	Weak transcription	Adipose Nuclei	Adipose
41	chr1:94087400-94092600	Genic enhancers	Hela-S3	cervix
42	chr1:94087600-94090800	Enhancers	HUVEC	blood vessel
43	chr1:94087800-94089200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:94087800-94090200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr1:94087800-94090400	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr1:94087800-94091600	Enhancers	Brain Germinal Matrix	brain
47	chr1:94087800-94092200	Enhancers	NHLF	lung
48	chr1:94088000-94089000	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr1:94088000-94089800	Enhancers	Osteobl	bone
50	chr1:94088000-94090400	Enhancers	Placenta Amnion	Placenta Amnion

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