Variant report

Variant	rs3813264
Chromosome Location	chr3:138189658-138189659
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	chr3:138185730..138189738-chr3:138190908..138194397,4	MCF-7	breast:
2	chr3:138186020..138187574-chr3:138189253..138191029,2	K562	blood:

Variant related genes	Relation type
ENSG00000158220	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10935282	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11709290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11916525	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12490633	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs12630060	0.82[JPT][hapmap]
rs12632794	0.82[JPT][hapmap]
rs12635490	0.86[JPT][hapmap]
rs12635904	0.82[JPT][hapmap]
rs12636246	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs12636910	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs12637679	0.82[JPT][hapmap]
rs13059817	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs13062423	0.82[JPT][hapmap]
rs13084780	0.82[JPT][hapmap]
rs13098554	0.82[JPT][hapmap]
rs13098789	0.82[ASN][1000 genomes]
rs1563615	0.82[JPT][hapmap]
rs1625751	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1672927	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs1672928	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1672932	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1673608	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs1673622	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1679165	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1679168	0.87[TSI][hapmap]
rs1679169	0.96[ASN][1000 genomes]
rs1720833	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2086351	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2347469	0.87[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs28719641	0.80[ASN][1000 genomes]
rs35471402	0.83[ASN][1000 genomes]
rs3884240	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3884241	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4678266	0.88[ASN][1000 genomes]
rs4678420	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs497334	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs503922	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs529615	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs542010	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs56236670	0.81[ASN][1000 genomes]
rs564800	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs609797	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs6439809	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6439810	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs66644444	0.88[ASN][1000 genomes]
rs67037472	0.89[ASN][1000 genomes]
rs6762114	0.82[ASN][1000 genomes]
rs6763380	0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs6771237	0.81[ASN][1000 genomes]
rs73229526	0.81[ASN][1000 genomes]
rs7626226	0.83[ASN][1000 genomes]
rs7645920	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs773450	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs774008	0.87[CEU][hapmap]
rs774011	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs774012	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs808925	0.84[CEU][hapmap]
rs814022	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs9049	0.82[JPT][hapmap]
rs936316	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs9822037	0.83[ASN][1000 genomes]
rs9823182	0.81[ASN][1000 genomes]
rs9848938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9855306	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3813264	CEP70	cis	parietal	SCAN
rs3813264	FAIM	cis	parietal	SCAN
rs3813264	CEP70	cis	Muscle Skeletal	GTEx
rs3813264	FAIM	cis	Muscle Skeletal	GTEx
rs3813264	CLDN18	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138161600-138198400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:138170800-138198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:138171000-138193000	Weak transcription	Pancreas	Pancrea
4	chr3:138171400-138198400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:138175200-138196000	Weak transcription	Brain Anterior Caudate	brain
6	chr3:138177600-138195400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:138178000-138197000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:138178200-138196000	Weak transcription	Aorta	Aorta
9	chr3:138179800-138199400	Weak transcription	Thymus	Thymus
10	chr3:138181200-138192400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:138184400-138191200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:138184400-138198400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:138185000-138195200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:138186200-138190200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:138186400-138190200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:138187000-138190200	Enhancers	Rectal Smooth Muscle	rectum
17	chr3:138187000-138190400	Enhancers	Colon Smooth Muscle	Colon
18	chr3:138187400-138191000	Enhancers	NHDF-Ad	bronchial
19	chr3:138187600-138197000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:138187800-138189800	Enhancers	Stomach Smooth Muscle	stomach
21	chr3:138188000-138210800	Weak transcription	Lung	lung
22	chr3:138188000-138211600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:138188200-138196200	Strong transcription	Fetal Muscle Leg	muscle
24	chr3:138188200-138197400	Weak transcription	HSMM	muscle
25	chr3:138188200-138197600	Weak transcription	HSMMtube	muscle
26	chr3:138188400-138189800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:138188400-138190200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:138188400-138191600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:138188400-138196400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:138188800-138190000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:138188800-138190200	Enhancers	Fetal Heart	heart
32	chr3:138189000-138189800	Enhancers	Left Ventricle	heart
33	chr3:138189000-138195200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:138189000-138195400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:138189400-138190000	Enhancers	Psoas Muscle	Psoas
36	chr3:138189400-138190000	Enhancers	Right Ventricle	heart
37	chr3:138189600-138190400	Weak transcription	Fetal Stomach	stomach
38	chr3:138189600-138191200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:138189600-138191200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:138189600-138198400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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