Variant report

Variant	rs2818169
Chromosome Location	chr1:94285049-94285050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94095273..94097251-chr1:94284521..94286111,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10489602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10489603	0.91[GIH][hapmap]
rs10489604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10782966	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10782967	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11165020	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11165022	0.83[JPT][hapmap]
rs11165024	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11165026	0.83[JPT][hapmap]
rs12027630	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12041975	0.83[JPT][hapmap]
rs12122113	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12123957	0.82[EUR][1000 genomes]
rs12134359	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12137687	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12140446	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs12143274	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12143279	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12563731	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12565614	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12565817	0.91[GIH][hapmap]
rs12566531	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12734571	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12739186	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12745990	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1398798	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1884018	0.96[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1980083	0.81[CEU][hapmap]
rs2143990	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2143992	0.83[JPT][hapmap]
rs2235971	0.86[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2391315	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs2391322	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs2747039	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2747041	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2747043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2747045	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2747050	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2818160	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2818162	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2818164	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3000471	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747965	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4075523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4141736	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4141737	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4240955	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4240956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4314890	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4350209	0.86[ASW][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs4847253	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4847256	0.85[CEU][hapmap]
rs4847264	0.83[JPT][hapmap]
rs6663218	0.82[JPT][hapmap]
rs6664719	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6681265	0.82[JPT][hapmap]
rs6685747	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7364910	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs743111	0.82[JPT][hapmap]
rs8179391	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs871854	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546822	chr1:94246577-94289863	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1815663	chr1:94246577-94291252	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1877	chr1:94247756-94292908	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv508415	chr1:94256122-94305339	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1802380	chr1:94272119-94291252	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1822452	chr1:94278128-94320233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2818169	RP11-488P3.1	cis	Nerve Tibial	GTEx
rs2818169	RP11-488P3.1	cis	lung	GTEx
rs2818169	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs2818169	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2818169	RP11-488P3.1	cis	Stomach	GTEx
rs2818169	RP11-488P3.1	cis	Artery Tibial	GTEx
rs2818169	RP11-488P3.1	cis	Thyroid	GTEx
rs2818169	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs2818169	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs2818169	RP11-488P3.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94276000-94285200	Enhancers	Placenta	Placenta
2	chr1:94279600-94302800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:94280000-94285600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:94280000-94290000	Weak transcription	Brain Angular Gyrus	brain
5	chr1:94280800-94285800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:94281200-94289600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:94281400-94285600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:94281400-94285800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:94281600-94285400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:94281800-94285600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:94282400-94285800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr1:94283000-94285400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:94283000-94285600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:94283000-94286000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:94283000-94288400	Weak transcription	NHDF-Ad	bronchial
16	chr1:94283200-94286000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:94283200-94286600	Weak transcription	A549	lung
18	chr1:94283200-94286800	Weak transcription	HSMMtube	muscle
19	chr1:94283400-94285800	Weak transcription	NH-A	brain
20	chr1:94283400-94286800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:94283400-94290000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:94283400-94310000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:94283600-94286800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:94283600-94286800	Weak transcription	Right Atrium	heart
25	chr1:94283600-94286800	Weak transcription	HSMM	muscle
26	chr1:94283600-94287800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:94283600-94288400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:94283600-94293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:94284000-94285600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:94284000-94285800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:94284000-94294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:94284200-94286000	Weak transcription	HUVEC	blood vessel
33	chr1:94284200-94286400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:94284200-94292200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:94284200-94306200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:94284200-94311200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:94284400-94285200	Enhancers	NHEK	skin
38	chr1:94284400-94285400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:94284400-94285600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:94284400-94286600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:94284400-94287400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:94284400-94289600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:94284400-94296000	Weak transcription	Fetal Intestine Small	intestine
44	chr1:94284600-94287000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:94284800-94285200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:94284800-94285200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:94285000-94286000	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr1:94285000-94286200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:94285000-94287000	Weak transcription	HMEC	breast
50	chr1:94285000-94287400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links