Variant report

Variant	rs3777179
Chromosome Location	chr5:95268768-95268769
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	chr5:95268201..95271259-chr5:95293634..95296677,4	K562	blood:
2	chr5:95268077..95269800-chr5:95402716..95405377,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10035477	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs10052503	0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10069748	0.84[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap]
rs10073752	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1043381	0.84[CEU][hapmap]
rs10515232	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1057963	0.83[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap]
rs1057964	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap]
rs11135442	0.84[CEU][hapmap];0.88[MEX][hapmap]
rs11738945	0.83[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs11741590	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap]
rs11742959	0.82[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs11744881	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs12055262	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1423268	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs1423269	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs1458017	0.83[CHB][hapmap]
rs1458018	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap]
rs17085231	0.84[CEU][hapmap];0.88[MEX][hapmap]
rs17085249	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs17085333	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17085428	0.81[JPT][hapmap]
rs1841010	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs1862313	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042340	0.83[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap]
rs2112566	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2161318	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2270554	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap]
rs2348984	0.80[CEU][hapmap];0.85[CHB][hapmap]
rs2546199	0.87[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2548594	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap]
rs3734131	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756703	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777162	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777163	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777165	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777166	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]
rs3777167	0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs3777168	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777171	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777173	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777175	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]
rs3777178	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777182	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3777183	0.82[CHB][hapmap];0.83[JPT][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3777184	0.84[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap]
rs3777185	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs3777188	0.81[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap]
rs3777189	0.84[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777190	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.85[YRI][hapmap]
rs3777193	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3777194	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap]
rs3777196	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap]
rs3777200	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs3777204	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs3777207	0.93[TSI][hapmap]
rs3815768	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap]
rs3822750	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4538631	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4642392	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap]
rs55841351	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56002885	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57243277	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57595413	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58921760	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59307279	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6556893	0.84[CEU][hapmap]
rs6556894	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6556898	0.83[ASN][1000 genomes]
rs6861531	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6877821	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6879652	0.84[CEU][hapmap]
rs6881355	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6881872	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6883880	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885567	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs6889029	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs6890954	0.83[CEU][hapmap]
rs6894651	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6897997	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6898371	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6898399	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72656689	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7700895	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7705279	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs7705720	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7710422	0.87[ASN][1000 genomes]
rs7716691	0.87[CEU][hapmap]
rs7724599	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[EUR][1000 genomes]
rs889302	0.83[CHB][hapmap]
rs918629	0.93[TSI][hapmap]
rs9314162	0.84[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs967546	0.84[CEU][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3777179	ELL2	Cis_1M	lymphoblastoid	RTeQTL
rs3777179	ELL2	cis	multi-tissue	Pritchard
rs3777179	ELL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95236400-95276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:95238200-95282000	Weak transcription	HUVEC	blood vessel
3	chr5:95243400-95278800	Weak transcription	Lung	lung
4	chr5:95243600-95274200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:95249800-95271600	Weak transcription	NH-A	brain
6	chr5:95252200-95272400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:95253800-95272400	Weak transcription	Placenta	Placenta
8	chr5:95257400-95276600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:95259400-95271400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:95259400-95271400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:95259400-95273400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:95259400-95274600	Weak transcription	Psoas Muscle	Psoas
13	chr5:95259800-95270000	Weak transcription	Right Ventricle	heart
14	chr5:95260000-95272200	Weak transcription	Left Ventricle	heart
15	chr5:95260000-95280600	Weak transcription	Esophagus	oesophagus
16	chr5:95260800-95273400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:95260800-95295200	Weak transcription	Primary T cells from cord blood	blood
18	chr5:95261600-95271200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr5:95261800-95271600	Weak transcription	Adipose Nuclei	Adipose
20	chr5:95262200-95272400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:95262200-95295400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr5:95262600-95271400	Weak transcription	Primary B cells from cord blood	blood
23	chr5:95263800-95278400	Weak transcription	Colonic Mucosa	Colon
24	chr5:95264200-95269200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:95264200-95271600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:95264800-95272400	Weak transcription	Stomach Mucosa	stomach
27	chr5:95264800-95275200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:95264800-95276000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:95264800-95279800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:95264800-95285600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:95264800-95293800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr5:95265000-95270000	Weak transcription	Fetal Intestine Small	intestine
33	chr5:95265000-95270000	Weak transcription	Ovary	ovary
34	chr5:95265000-95270000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:95265000-95272200	Weak transcription	Gastric	stomach
36	chr5:95265000-95272200	Weak transcription	Pancreas	Pancrea
37	chr5:95265000-95285600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr5:95265400-95270200	Enhancers	Brain Cingulate Gyrus	brain
39	chr5:95265400-95281800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:95265800-95270400	Enhancers	Brain Substantia Nigra	brain
41	chr5:95266000-95269000	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr5:95266200-95270200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:95266400-95268800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:95266600-95269000	Enhancers	Brain Hippocampus Middle	brain
45	chr5:95266600-95269200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:95266600-95270600	Enhancers	Brain Angular Gyrus	brain
47	chr5:95266600-95274400	Weak transcription	NHLF	lung
48	chr5:95267000-95270400	Enhancers	NHEK	skin
49	chr5:95267000-95272600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:95267000-95277000	Weak transcription	Fetal Thymus	thymus

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