Variant report

Variant	rs11719468
Chromosome Location	chr3:99671848-99671849
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99670705..99673517-chr3:99675233..99678089,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10936003	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12488245	0.81[CEU][hapmap]
rs1287284	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs13059754	0.84[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1384062	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1387647	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs1610509	0.94[JPT][hapmap]
rs16841874	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs1718235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4577503	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4928150	0.84[CEU][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4928151	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs4928153	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs4928230	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4928237	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs58704213	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440967	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs6802817	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs6806323	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs704571	0.94[JPT][hapmap]
rs704572	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs704574	0.94[JPT][hapmap]
rs7613864	0.83[ASN][1000 genomes]
rs7619512	0.81[EUR][1000 genomes]
rs7649349	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs7650727	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs766778	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs792831	0.94[JPT][hapmap]
rs792833	0.82[JPT][hapmap]
rs792835	0.94[JPT][hapmap]
rs792836	0.94[JPT][hapmap]
rs792837	0.94[JPT][hapmap]
rs793437	0.82[ASN][1000 genomes]
rs793439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793443	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs793446	0.85[CEU][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs793456	0.80[ASN][1000 genomes]
rs793464	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs793475	0.84[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs793476	0.85[ASN][1000 genomes]
rs793482	0.85[YRI][hapmap]
rs793483	0.94[JPT][hapmap]
rs793485	0.94[JPT][hapmap]
rs793497	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs793502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs796976	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs813218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs902159	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs923472	0.85[CEU][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11719468	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99657600-99686600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:99664400-99672200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:99664400-99672600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:99664400-99672600	Weak transcription	Gastric	stomach
5	chr3:99664400-99674800	Weak transcription	Right Atrium	heart
6	chr3:99664600-99672200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:99664600-99676200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:99664800-99672600	Weak transcription	Left Ventricle	heart
9	chr3:99664800-99672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:99664800-99677200	Weak transcription	Esophagus	oesophagus
11	chr3:99664800-99677200	Weak transcription	Ovary	ovary
12	chr3:99665000-99672400	Weak transcription	Fetal Heart	heart
13	chr3:99665000-99677200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:99665000-99677200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:99665000-99678800	Weak transcription	Aorta	Aorta
16	chr3:99665200-99673800	Weak transcription	Fetal Lung	lung
17	chr3:99666400-99672200	Weak transcription	Psoas Muscle	Psoas
18	chr3:99667800-99672200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:99669200-99672600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:99669200-99679800	Weak transcription	Fetal Intestine Small	intestine
21	chr3:99669400-99673200	Enhancers	NH-A	brain
22	chr3:99669800-99672800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:99669800-99673000	Enhancers	Osteobl	bone
24	chr3:99669800-99673200	Enhancers	HSMMtube	muscle
25	chr3:99670000-99672600	Weak transcription	Pancreas	Pancrea
26	chr3:99670000-99672800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr3:99670000-99673000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:99670200-99672000	Weak transcription	Stomach Mucosa	stomach
29	chr3:99670200-99672600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:99670200-99672600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:99670400-99676000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:99670600-99672000	Weak transcription	K562	blood
33	chr3:99670600-99672600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:99670600-99672600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:99670800-99672000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:99670800-99679200	Weak transcription	Small Intestine	intestine
37	chr3:99671200-99672200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:99671200-99672600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:99671200-99672600	Weak transcription	NHDF-Ad	bronchial
40	chr3:99671200-99672800	Weak transcription	NHLF	lung
41	chr3:99671400-99672600	Weak transcription	HepG2	liver
42	chr3:99671400-99673000	Weak transcription	A549	lung
43	chr3:99671400-99679400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:99671600-99672000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:99671600-99684200	Weak transcription	NHEK	skin
46	chr3:99671600-99688200	Weak transcription	Primary T cells from cord blood	blood
47	chr3:99671800-99672600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:99671800-99673000	Enhancers	HSMM	muscle
49	chr3:99671800-99676400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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