Variant report

Variant	rs4930394
Chromosome Location	chr11:66680543-66680544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66661363..66663276-chr11:66678554..66680606,2	MCF-7	breast:
2	chr11:66679281..66682230-chr11:66683799..66685977,2	MCF-7	breast:
3	chr11:66678730..66681297-chr11:66687110..66688715,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239099	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1077256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791896	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11227624	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227625	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs11227628	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11227630	0.86[ASN][1000 genomes]
rs1530891	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1901376	0.91[ASN][1000 genomes]
rs34482178	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4483596	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4930393	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6591226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67156018	0.89[ASN][1000 genomes]
rs7107498	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs7110302	0.87[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs7119682	0.82[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs746018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs746019	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935749	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7936290	0.86[ASN][1000 genomes]
rs7944999	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs7952017	0.91[ASN][1000 genomes]
rs966021	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
5	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4930394	FGF4	cis	parietal	SCAN
rs4930394	EHBP1L1	cis	cerebellum	SCAN
rs4930394	PC	cis	cerebellum	SCAN
rs4930394	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs4930394	B3GNT1	cis	parietal	SCAN
rs4930394	SLC25A45	cis	parietal	SCAN
rs4930394	CDC42BPG	cis	cerebellum	SCAN
rs4930394	ACTN3	cis	Muscle Skeletal	GTEx
rs4930394	SUV420H1	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66672200-66684000	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr11:66672600-66683000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr11:66674000-66687000	Weak transcription	HSMMtube	muscle
4	chr11:66674400-66689600	Weak transcription	NHLF	lung
5	chr11:66674600-66684800	Weak transcription	Fetal Stomach	stomach
6	chr11:66674600-66696400	Weak transcription	NHEK	skin
7	chr11:66675000-66696200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:66675400-66681400	Weak transcription	Fetal Intestine Large	intestine
9	chr11:66675600-66682000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:66675600-66683000	Weak transcription	A549	lung
11	chr11:66675600-66687000	Weak transcription	Osteobl	bone
12	chr11:66675600-66699800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:66675800-66682200	Weak transcription	Fetal Intestine Small	intestine
14	chr11:66676200-66682000	Weak transcription	K562	blood
15	chr11:66676200-66682400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:66676200-66688600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:66676400-66682600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:66676800-66682400	Weak transcription	Gastric	stomach
19	chr11:66676800-66683800	Weak transcription	Fetal Brain Female	brain
20	chr11:66676800-66696400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:66677000-66683000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:66677200-66682400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:66677200-66683400	Weak transcription	Liver	Liver
24	chr11:66677200-66692000	Weak transcription	Pancreas	Pancrea
25	chr11:66678000-66682800	Enhancers	Brain Hippocampus Middle	brain
26	chr11:66678000-66688600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr11:66678400-66683600	Weak transcription	Hela-S3	cervix
28	chr11:66678800-66682800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:66679400-66680600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr11:66679400-66680600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr11:66679400-66680800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr11:66679600-66680600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr11:66679600-66680600	Enhancers	H9 Cell Line	embryonic stem cell
34	chr11:66679600-66680600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr11:66679600-66680600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr11:66679600-66680800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr11:66679600-66680800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr11:66679600-66680800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:66679600-66681000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:66679600-66681400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:66679600-66681400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:66679800-66680600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr11:66679800-66680600	Enhancers	Spleen	Spleen
44	chr11:66679800-66680800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:66679800-66681400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:66679800-66681400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr11:66679800-66681600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr11:66680000-66680600	Enhancers	Brain Germinal Matrix	brain
49	chr11:66680000-66680600	Enhancers	Fetal Muscle Trunk	muscle
50	chr11:66680000-66680600	Enhancers	Stomach Mucosa	stomach

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