Variant report

Variant	rs3777175
Chromosome Location	chr5:95277555-95277556
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	chr5:95276300..95278479-chr5:95281336..95283679,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10052503	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10069748	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs10073752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10515232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1057963	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs1057964	0.83[CHB][hapmap]
rs11738945	0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs11741590	0.83[CHB][hapmap]
rs11742959	0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs11744881	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs12055262	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1423268	0.83[CHB][hapmap]
rs1423269	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs1458017	0.83[CHB][hapmap]
rs1458018	0.83[CHB][hapmap]
rs17085231	0.82[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs17085249	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap]
rs17085333	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17085428	0.81[JPT][hapmap]
rs1841010	0.83[CHB][hapmap]
rs1862313	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2042340	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs2112566	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2161318	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2270554	0.83[CHB][hapmap]
rs2348984	0.85[CHB][hapmap]
rs2546199	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2548594	0.83[CHB][hapmap]
rs3734131	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756703	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777162	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777163	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777164	0.82[EUR][1000 genomes]
rs3777165	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777167	0.84[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs3777168	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777171	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777173	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777178	0.87[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3777179	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777182	0.83[ASN][1000 genomes]
rs3777183	0.82[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs3777184	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777185	0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap]
rs3777188	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs3777189	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777190	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs3777193	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3777194	0.83[CHB][hapmap]
rs3777196	0.83[CHB][hapmap]
rs3777200	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap]
rs3777204	0.83[CHB][hapmap]
rs3777207	0.86[TSI][hapmap]
rs3815768	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs3822750	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4538631	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4642392	0.83[CHB][hapmap]
rs55841351	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56002885	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57243277	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57595413	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58921760	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59307279	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6556894	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6556898	0.83[ASN][1000 genomes]
rs6861531	0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6877821	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6881355	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6881872	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6883880	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6885567	0.83[CHB][hapmap]
rs6889029	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap]
rs6894651	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6897997	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6898371	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6898399	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72656689	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7700895	0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7705279	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7705720	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7710422	0.87[ASN][1000 genomes]
rs7724599	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[EUR][1000 genomes]
rs889302	0.83[CHB][hapmap]
rs918629	1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9314162	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs967546	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3777175	ELL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95238200-95282000	Weak transcription	HUVEC	blood vessel
2	chr5:95243400-95278800	Weak transcription	Lung	lung
3	chr5:95260000-95280600	Weak transcription	Esophagus	oesophagus
4	chr5:95260800-95295200	Weak transcription	Primary T cells from cord blood	blood
5	chr5:95262200-95295400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:95263800-95278400	Weak transcription	Colonic Mucosa	Colon
7	chr5:95264800-95279800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:95264800-95285600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:95264800-95293800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr5:95265000-95285600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr5:95265400-95281800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:95267200-95280200	Weak transcription	Aorta	Aorta
13	chr5:95267400-95280000	Weak transcription	A549	lung
14	chr5:95270000-95283200	Genic enhancers	Muscle Satellite Cultured Cells	--
15	chr5:95270400-95284800	Weak transcription	Fetal Intestine Small	intestine
16	chr5:95270400-95285400	Weak transcription	Right Ventricle	heart
17	chr5:95270800-95279200	Genic enhancers	HepG2	liver
18	chr5:95271400-95278800	Genic enhancers	NHEK	skin
19	chr5:95272200-95277800	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr5:95272200-95278800	Enhancers	Brain Angular Gyrus	brain
21	chr5:95272400-95278800	Enhancers	Brain Hippocampus Middle	brain
22	chr5:95272400-95283800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:95272600-95283400	Enhancers	Brain Substantia Nigra	brain
24	chr5:95272800-95277800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:95272800-95291200	Weak transcription	NH-A	brain
26	chr5:95273000-95287600	Weak transcription	Primary B cells from cord blood	blood
27	chr5:95273000-95291200	Weak transcription	HSMMtube	muscle
28	chr5:95273600-95280200	Weak transcription	Gastric	stomach
29	chr5:95273800-95285600	Weak transcription	Stomach Mucosa	stomach
30	chr5:95274400-95279200	Genic enhancers	Liver	Liver
31	chr5:95274600-95277600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:95274600-95279000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:95274600-95280200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr5:95274800-95292200	Weak transcription	Placenta	Placenta
35	chr5:95275000-95277600	Enhancers	Brain Germinal Matrix	brain
36	chr5:95275000-95277800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr5:95275000-95279600	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr5:95275200-95278800	Strong transcription	Hela-S3	cervix
39	chr5:95275400-95291400	Weak transcription	NHDF-Ad	bronchial
40	chr5:95275600-95278000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:95275800-95277600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:95275800-95277800	Genic enhancers	HMEC	breast
43	chr5:95276000-95277600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr5:95276000-95277800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:95276000-95278800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:95276200-95277600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:95276200-95277800	Enhancers	H1 Cell Line	embryonic stem cell
48	chr5:95276200-95277800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:95276200-95277800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:95276200-95277800	Genic enhancers	Osteobl	bone

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