Variant report

Variant	rs3777166
Chromosome Location	chr5:95291056-95291057
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95290720..95292319-chr5:96270135..96272344,2	MCF-7	breast:
2	chr5:95289886..95294659-chr5:95295662..95298234,5	MCF-7	breast:
3	chr5:95282858..95287226-chr5:95287357..95291460,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247121	Chromatin interaction
ENSG00000113441	Chromatin interaction
ENSG00000251314	Chromatin interaction
ENSG00000118985	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10052503	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10069748	0.83[CHB][hapmap]
rs10073752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1057963	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs1057964	0.83[CHB][hapmap]
rs11738945	0.87[JPT][hapmap]
rs11741590	0.83[CHB][hapmap]
rs11742959	0.87[JPT][hapmap]
rs11744881	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs12055262	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1423268	0.84[CHB][hapmap]
rs1423269	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs1458017	0.83[CHB][hapmap]
rs1458018	0.83[CHB][hapmap]
rs17085231	0.86[YRI][hapmap]
rs17085249	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs17085333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085428	0.81[JPT][hapmap]
rs1841010	0.84[CHB][hapmap]
rs1862313	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042340	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs2112566	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161318	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2270554	0.83[CHB][hapmap]
rs2348984	0.86[CHB][hapmap]
rs2546199	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548594	0.83[CHB][hapmap]
rs3734131	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756703	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777162	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777163	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777164	0.83[EUR][1000 genomes]
rs3777165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777167	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs3777168	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777175	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]
rs3777178	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777179	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777182	0.85[ASN][1000 genomes]
rs3777183	0.83[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs3777184	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777185	0.91[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap]
rs3777188	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777189	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777190	0.91[CHB][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];0.88[JPT][hapmap];0.85[YRI][hapmap]
rs3777204	0.84[CHB][hapmap]
rs3815768	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3822750	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4538631	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4642392	0.83[CHB][hapmap]
rs55841351	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56002885	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57243277	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57595413	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58921760	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59307279	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6556894	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6556898	0.84[ASN][1000 genomes]
rs6861531	0.89[CEU][hapmap];0.91[CHB][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6877821	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6881355	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6881872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6883880	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6885567	0.84[CHB][hapmap]
rs6889029	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs6894651	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6897997	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6898371	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6898399	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72656689	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7700895	0.89[CEU][hapmap];0.91[CHB][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7705279	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[EUR][1000 genomes]
rs7705720	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710422	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7724599	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes]
rs889302	0.84[CHB][hapmap]
rs918629	0.83[EUR][1000 genomes]
rs9314162	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs967546	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
rs3777166	ELL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95260800-95295200	Weak transcription	Primary T cells from cord blood	blood
2	chr5:95262200-95295400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:95264800-95293800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr5:95272800-95291200	Weak transcription	NH-A	brain
5	chr5:95273000-95291200	Weak transcription	HSMMtube	muscle
6	chr5:95274800-95292200	Weak transcription	Placenta	Placenta
7	chr5:95275400-95291400	Weak transcription	NHDF-Ad	bronchial
8	chr5:95277200-95291600	Weak transcription	Ovary	ovary
9	chr5:95277800-95291600	Weak transcription	Fetal Intestine Large	intestine
10	chr5:95278000-95292200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:95281000-95291600	Weak transcription	Aorta	Aorta
12	chr5:95281000-95291600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:95281000-95294000	Weak transcription	Esophagus	oesophagus
14	chr5:95282400-95291200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:95282400-95294000	Weak transcription	Pancreas	Pancrea
16	chr5:95282600-95294000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:95284600-95295200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:95284800-95292000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:95286000-95293800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:95286400-95291600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:95286400-95295200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:95287000-95294800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:95287600-95291200	Weak transcription	Psoas Muscle	Psoas
24	chr5:95287600-95291800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:95288000-95291600	Weak transcription	Primary B cells from cord blood	blood
26	chr5:95288000-95294400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:95288600-95291800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:95288600-95292800	Enhancers	Fetal Brain Male	brain
29	chr5:95289200-95294000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:95289600-95291200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:95289800-95291400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:95290400-95291400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:95290400-95291400	Genic enhancers	HepG2	liver
34	chr5:95290400-95292000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr5:95290400-95293000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:95290400-95294000	Active TSS	Right Ventricle	heart
37	chr5:95290600-95291200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:95290600-95291200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr5:95290600-95291200	Genic enhancers	NHEK	skin
40	chr5:95290600-95291200	Genic enhancers	Osteobl	bone
41	chr5:95290600-95291400	Genic enhancers	HMEC	breast
42	chr5:95290600-95291400	Genic enhancers	HSMM	muscle
43	chr5:95290600-95291600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:95290600-95291600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:95290600-95291600	Enhancers	Brain Anterior Caudate	brain
46	chr5:95290600-95291600	Enhancers	Brain Hippocampus Middle	brain
47	chr5:95290600-95291600	Weak transcription	Left Ventricle	heart
48	chr5:95290600-95292000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
49	chr5:95290600-95292600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:95290600-95293000	Enhancers	Colon Smooth Muscle	Colon

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