Variant report

Variant	rs7716691
Chromosome Location	chr5:95237040-95237041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr5:95235811-95237143	SK-N-SH	brain:	n/a	chr5:95236876-95236884
2	POLR2A	chr5:95236216-95242396	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ELL2	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10035477	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10052503	0.91[YRI][hapmap]
rs10069748	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070197	0.94[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1043381	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1057963	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1057964	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11135441	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs11135442	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11738768	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11738945	0.88[CEU][hapmap]
rs11739652	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11741563	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11741590	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742959	0.87[CEU][hapmap]
rs11744881	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13361341	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13361837	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1423268	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1423269	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1458017	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1458018	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1458019	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs147295	0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs154460	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17085231	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs17085249	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17085266	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1841010	1.00[CEU][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2015159	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2042340	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2270554	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2348984	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2546191	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2547997	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548594	1.00[CEU][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2829	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777162	0.83[YRI][hapmap]
rs3777163	0.84[YRI][hapmap]
rs3777178	0.80[CEU][hapmap]
rs3777179	0.87[CEU][hapmap]
rs3777182	0.90[EUR][1000 genomes]
rs3777183	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3777184	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777185	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777188	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777189	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777190	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777192	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777193	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777194	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777196	1.00[CEU][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777197	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777200	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777201	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777202	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777203	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777204	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777207	0.92[CEU][hapmap]
rs3777208	0.96[EUR][1000 genomes]
rs3815768	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4563648	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4642392	1.00[CEU][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56156268	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56219066	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6556893	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6861531	0.82[CEU][hapmap];0.84[YRI][hapmap]
rs6877329	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6879652	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6885567	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6889029	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6890954	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7700895	0.82[CEU][hapmap]
rs7702674	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs889302	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9314162	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs967546	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9986236	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

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
rs7716691	ELL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95213000-95244600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:95214400-95247800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:95214400-95251800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:95215800-95244600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:95218000-95242200	Weak transcription	Spleen	Spleen
6	chr5:95218200-95246200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr5:95219800-95244400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:95220000-95242000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:95220000-95245200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr5:95220600-95243200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:95220800-95237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:95220800-95237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:95220800-95240800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:95221600-95252200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr5:95222000-95241600	Strong transcription	GM12878-XiMat	blood
16	chr5:95222000-95252200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:95223000-95259800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:95223400-95237600	Strong transcription	Placenta	Placenta
19	chr5:95224000-95237600	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:95224200-95237600	Weak transcription	Stomach Mucosa	stomach
21	chr5:95226000-95237600	Weak transcription	Fetal Kidney	kidney
22	chr5:95226400-95263600	Weak transcription	Colonic Mucosa	Colon
23	chr5:95227400-95251600	Weak transcription	Primary T cells from cord blood	blood
24	chr5:95227400-95253800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:95227600-95242400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr5:95227600-95244600	Weak transcription	Small Intestine	intestine
27	chr5:95230800-95237800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:95231200-95254000	Weak transcription	Fetal Stomach	stomach
29	chr5:95231800-95237400	Weak transcription	Right Atrium	heart
30	chr5:95231800-95239600	Weak transcription	Left Ventricle	heart
31	chr5:95231800-95242200	Weak transcription	Pancreas	Pancrea
32	chr5:95231800-95242400	Weak transcription	Right Ventricle	heart
33	chr5:95231800-95243200	Weak transcription	Lung	lung
34	chr5:95231800-95244200	Weak transcription	Ovary	ovary
35	chr5:95232000-95238400	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr5:95232200-95244600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:95232400-95255200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr5:95232600-95237400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr5:95232600-95244600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr5:95232600-95247400	Weak transcription	Aorta	Aorta
41	chr5:95232800-95237200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr5:95232800-95240600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr5:95232800-95242000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:95232800-95242200	Weak transcription	Gastric	stomach
45	chr5:95232800-95243000	Weak transcription	Esophagus	oesophagus
46	chr5:95232800-95244200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr5:95232800-95244600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:95234200-95251800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr5:95234400-95244800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:95234400-95251800	Weak transcription	Fetal Thymus	thymus

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