Variant report

Variant	rs3777183
Chromosome Location	chr5:95263735-95263736
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	chr5:95262626..95265334-chr5:95402014..95404790,2	K562	blood:
2	chr5:95263040..95265383-chr5:95296310..95298391,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLRX-4	chr5:95263669-95263880	expReg_chr5_5250_-

Variant related genes	Relation type
ENSG00000251314	Chromatin interaction
ENSG00000118985	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10035477	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs10052503	0.83[CHB][hapmap]
rs10069748	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs10070197	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs10073752	0.83[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs1043381	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs10515232	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs1057963	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1057964	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[EUR][1000 genomes]
rs11135441	0.95[CEU][hapmap]
rs11135442	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs11738768	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11738945	0.81[CEU][hapmap]
rs11739652	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11741563	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11741590	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs11744881	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13361341	0.93[EUR][1000 genomes]
rs13361837	0.93[EUR][1000 genomes]
rs1423268	0.95[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs1423269	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1458017	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1458018	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[EUR][1000 genomes]
rs1458019	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17085231	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs17085249	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17085266	0.93[EUR][1000 genomes]
rs17085333	0.82[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs1841010	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[EUR][1000 genomes]
rs1862313	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2015159	0.97[EUR][1000 genomes]
rs2042340	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2112566	0.85[ASN][1000 genomes]
rs2161318	0.82[CHB][hapmap]
rs2270554	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[EUR][1000 genomes]
rs2348984	0.94[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes]
rs2546191	0.89[EUR][1000 genomes]
rs2546199	0.82[CHB][hapmap]
rs2547997	0.93[EUR][1000 genomes]
rs2548594	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[EUR][1000 genomes]
rs2829	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3734131	0.85[ASN][1000 genomes]
rs3777162	0.82[CHB][hapmap]
rs3777163	0.83[CHB][hapmap]
rs3777165	0.82[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs3777166	0.83[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs3777168	0.83[ASN][1000 genomes]
rs3777171	0.82[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs3777173	0.82[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs3777175	0.82[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs3777178	0.83[CHB][hapmap]
rs3777179	0.82[CHB][hapmap];0.83[JPT][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3777182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777184	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777185	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777188	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777189	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777190	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777192	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777193	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs3777194	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[EUR][1000 genomes]
rs3777196	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[EUR][1000 genomes]
rs3777197	0.89[EUR][1000 genomes]
rs3777200	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3777201	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3777202	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3777203	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3777204	0.95[CEU][hapmap];0.92[CHB][hapmap];0.89[EUR][1000 genomes]
rs3777208	0.86[EUR][1000 genomes]
rs3815768	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4538631	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs4563648	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4642392	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[EUR][1000 genomes]
rs56002885	0.86[ASN][1000 genomes]
rs56156268	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56219066	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57243277	0.83[ASN][1000 genomes]
rs6556893	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs6861531	0.83[CHB][hapmap]
rs6877329	0.93[EUR][1000 genomes]
rs6879652	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs6881872	0.82[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs6883880	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6885567	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs6889029	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6890954	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs7700895	0.83[CHB][hapmap]
rs7702674	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7705720	0.85[ASN][1000 genomes]
rs7716691	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7724599	0.82[CHB][hapmap]
rs889302	0.95[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9314162	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs967546	0.95[CEU][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9986236	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
5	esv3371299	chr5:95261096-95265494	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3329367	chr5:95261896-95264644	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3421555	chr5:95262021-95264769	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3331990	chr5:95262346-95264544	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3777183	ELL2	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 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	chr5:95246400-95266400	Weak transcription	NHDF-Ad	bronchial
6	chr5:95249800-95271600	Weak transcription	NH-A	brain
7	chr5:95252200-95263800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:95252200-95272400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:95252400-95264600	Weak transcription	Ovary	ovary
10	chr5:95252400-95266400	Weak transcription	HSMMtube	muscle
11	chr5:95253800-95272400	Weak transcription	Placenta	Placenta
12	chr5:95254600-95266000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:95257400-95266400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:95257400-95276600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:95259000-95264000	Enhancers	Dnd41	blood
16	chr5:95259000-95264600	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr5:95259400-95264600	Weak transcription	Gastric	stomach
18	chr5:95259400-95264800	Enhancers	Primary B cells from peripheral blood	blood
19	chr5:95259400-95266800	Weak transcription	Aorta	Aorta
20	chr5:95259400-95271400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:95259400-95271400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:95259400-95273400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:95259400-95274600	Weak transcription	Psoas Muscle	Psoas
24	chr5:95259800-95270000	Weak transcription	Right Ventricle	heart
25	chr5:95260000-95264600	Weak transcription	Pancreas	Pancrea
26	chr5:95260000-95264600	Weak transcription	Right Atrium	heart
27	chr5:95260000-95272200	Weak transcription	Left Ventricle	heart
28	chr5:95260000-95280600	Weak transcription	Esophagus	oesophagus
29	chr5:95260800-95263800	Weak transcription	Small Intestine	intestine
30	chr5:95260800-95264200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr5:95260800-95264200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:95260800-95273400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:95260800-95295200	Weak transcription	Primary T cells from cord blood	blood
34	chr5:95261200-95264200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr5:95261200-95265800	Weak transcription	Brain Anterior Caudate	brain
36	chr5:95261400-95263800	Weak transcription	NHLF	lung
37	chr5:95261400-95264000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr5:95261400-95264200	Weak transcription	Stomach Mucosa	stomach
39	chr5:95261400-95266800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:95261400-95266800	Weak transcription	A549	lung
41	chr5:95261600-95264200	Weak transcription	Fetal Intestine Large	intestine
42	chr5:95261600-95264600	Weak transcription	Fetal Thymus	thymus
43	chr5:95261600-95266000	Weak transcription	HMEC	breast
44	chr5:95261600-95271200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr5:95261800-95263800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:95261800-95271600	Weak transcription	Adipose Nuclei	Adipose
47	chr5:95262000-95263800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:95262000-95264600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:95262000-95264600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:95262000-95265800	Weak transcription	Osteobl	bone

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