Variant report

Variant	rs3777201
Chromosome Location	chr5:95234630-95234631
allele	A/C
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	POLR2A	chr5:95234629-95234869	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ELL2	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10035477	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10069748	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10070197	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1043381	0.99[EUR][1000 genomes]
rs1057963	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1057964	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11135441	0.82[EUR][1000 genomes]
rs11135442	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11738768	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11739652	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11741563	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11741590	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11744881	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13361341	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13361837	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1423268	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1423269	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1458017	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1458018	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1458019	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs147295	0.83[EUR][1000 genomes]
rs154460	0.81[EUR][1000 genomes]
rs17085231	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17085249	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17085266	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1841010	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2015159	0.91[EUR][1000 genomes]
rs2042340	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2270554	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2348984	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2546191	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2547997	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2548594	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2829	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777182	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3777183	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3777184	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777185	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777188	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777189	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777190	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777192	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777193	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777194	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777196	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777197	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777200	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777202	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777203	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777204	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777208	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3815768	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4563648	0.91[EUR][1000 genomes]
rs4642392	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56156268	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56219066	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6556893	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6877329	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6879652	0.99[EUR][1000 genomes]
rs6885567	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6889029	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6890954	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7702674	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7716691	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs889302	0.91[EUR][1000 genomes]
rs9314162	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs967546	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9986236	0.94[EUR][1000 genomes];0.84[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

No data

Chromatin state (count:109 , 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	chr5:95220200-95235400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:95220400-95236800	Strong transcription	HMEC	breast
12	chr5:95220600-95236200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:95220600-95243200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:95220800-95235400	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr5:95220800-95235600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:95220800-95237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:95220800-95237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:95220800-95240800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:95221000-95236600	Strong transcription	NH-A	brain
20	chr5:95221400-95236200	Strong transcription	HSMM	muscle
21	chr5:95221600-95235800	Strong transcription	Osteobl	bone
22	chr5:95221600-95252200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr5:95222000-95241600	Strong transcription	GM12878-XiMat	blood
24	chr5:95222000-95252200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:95222800-95235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:95223000-95259800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:95223400-95237600	Strong transcription	Placenta	Placenta
28	chr5:95223800-95234800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:95223800-95237000	Strong transcription	NHEK	skin
30	chr5:95224000-95237600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:95224200-95237600	Weak transcription	Stomach Mucosa	stomach
32	chr5:95225000-95236400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:95226000-95236600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:95226000-95237600	Weak transcription	Fetal Kidney	kidney
35	chr5:95226400-95263600	Weak transcription	Colonic Mucosa	Colon
36	chr5:95227400-95236000	Strong transcription	Hela-S3	cervix
37	chr5:95227400-95251600	Weak transcription	Primary T cells from cord blood	blood
38	chr5:95227400-95253800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:95227600-95236400	Weak transcription	Colon Smooth Muscle	Colon
40	chr5:95227600-95242400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr5:95227600-95244600	Weak transcription	Small Intestine	intestine
42	chr5:95229400-95234800	Strong transcription	Liver	Liver
43	chr5:95229600-95236000	Strong transcription	NHDF-Ad	bronchial
44	chr5:95229600-95236600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr5:95229600-95236600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr5:95229800-95235800	Strong transcription	Adipose Nuclei	Adipose
47	chr5:95230400-95235600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:95230600-95235600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr5:95230600-95236600	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr5:95230800-95236800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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