Variant report

Variant	rs41276261
Chromosome Location	chr5:95236298-95236299
allele	C/G
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	chr5:95235934-95236460	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:95236231-95236520	ProgFib	skin:	n/a	n/a
3	POLR2A	chr5:95236087-95236338	GM12892	blood:	n/a	n/a
4	PRDM1	chr5:95236078-95236323	Hela-S3	cervix:	n/a	chr5:95236156-95236171
5	EP300	chr5:95235811-95237143	SK-N-SH	brain:	n/a	chr5:95236876-95236884
6	POLR2A	chr5:95236216-95242396	HepG2	liver:	n/a	n/a
7	YY1	chr5:95236082-95236402	SK-N-SH_RA	brain:	n/a	n/a
8	TCF12	chr5:95235954-95236635	SK-N-SH	brain:	n/a	n/a
9	NFIC	chr5:95235984-95236398	SK-N-SH	brain:	n/a	n/a
10	EP300	chr5:95236031-95236460	SK-N-SH_RA	brain:	n/a	n/a
11	REST	chr5:95236058-95236442	PFSK-1	brain:	n/a	n/a
12	GATA3	chr5:95235877-95236449	SK-N-SH	brain:	n/a	n/a
13	REST	chr5:95236115-95236427	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr5:95236057-95236577	SK-N-SH	brain:	n/a	n/a
15	TCF12	chr5:95235995-95236769	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr5:95236101-95236485	GM12892	blood:	n/a	n/a
17	POLR2A	chr5:95236159-95236372	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr5:95236211-95236362	HepG2	liver:	n/a	n/a
19	NFIC	chr5:95235828-95236591	SK-N-SH	brain:	n/a	n/a
20	GATA2	chr5:95235686-95236441	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
ELL2	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10428657	1.00[EUR][1000 genomes]
rs10428702	1.00[EUR][1000 genomes]
rs10515233	1.00[EUR][1000 genomes]
rs10515234	1.00[EUR][1000 genomes]
rs11948037	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12514954	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12517786	1.00[EUR][1000 genomes]
rs12522489	1.00[EUR][1000 genomes]
rs12523306	1.00[EUR][1000 genomes]
rs17085220	1.00[EUR][1000 genomes]
rs17085223	1.00[EUR][1000 genomes]
rs17085224	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085227	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085243	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17085339	1.00[EUR][1000 genomes]
rs17085366	1.00[EUR][1000 genomes]
rs17085373	1.00[EUR][1000 genomes]
rs17085393	1.00[EUR][1000 genomes]
rs17085426	1.00[EUR][1000 genomes]
rs28521883	1.00[EUR][1000 genomes]
rs3756701	1.00[EUR][1000 genomes]
rs3777174	1.00[EUR][1000 genomes]
rs3777176	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3777177	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3777180	1.00[EUR][1000 genomes]
rs55763081	1.00[EUR][1000 genomes]
rs56776515	1.00[EUR][1000 genomes]
rs58389685	1.00[EUR][1000 genomes]
rs60908902	1.00[EUR][1000 genomes]
rs61268106	1.00[EUR][1000 genomes]
rs6143071	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6556897	1.00[EUR][1000 genomes]
rs6861075	1.00[EUR][1000 genomes]
rs6870388	1.00[EUR][1000 genomes]
rs6872006	1.00[EUR][1000 genomes]
rs6874371	1.00[EUR][1000 genomes]
rs6891082	1.00[EUR][1000 genomes]
rs6891633	1.00[EUR][1000 genomes]
rs6893788	1.00[EUR][1000 genomes]
rs73771827	1.00[EUR][1000 genomes]
rs7700606	1.00[EUR][1000 genomes]
rs7724475	1.00[EUR][1000 genomes]
rs7736480	1.00[EUR][1000 genomes]
rs9687631	1.00[EUR][1000 genomes]
rs977128	1.00[EUR][1000 genomes]
rs977129	1.00[EUR][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	chr5:95220400-95236800	Strong transcription	HMEC	breast
11	chr5:95220600-95243200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:95220800-95237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:95220800-95237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:95220800-95240800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:95221000-95236600	Strong transcription	NH-A	brain
16	chr5:95221600-95252200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr5:95222000-95241600	Strong transcription	GM12878-XiMat	blood
18	chr5:95222000-95252200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:95223000-95259800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:95223400-95237600	Strong transcription	Placenta	Placenta
21	chr5:95223800-95237000	Strong transcription	NHEK	skin
22	chr5:95224000-95237600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr5:95224200-95237600	Weak transcription	Stomach Mucosa	stomach
24	chr5:95225000-95236400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:95226000-95236600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:95226000-95237600	Weak transcription	Fetal Kidney	kidney
27	chr5:95226400-95263600	Weak transcription	Colonic Mucosa	Colon
28	chr5:95227400-95251600	Weak transcription	Primary T cells from cord blood	blood
29	chr5:95227400-95253800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr5:95227600-95236400	Weak transcription	Colon Smooth Muscle	Colon
31	chr5:95227600-95242400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:95227600-95244600	Weak transcription	Small Intestine	intestine
33	chr5:95229600-95236600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr5:95229600-95236600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr5:95230600-95236600	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:95230800-95236800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:95230800-95237800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:95231000-95236800	Strong transcription	HUVEC	blood vessel
39	chr5:95231200-95254000	Weak transcription	Fetal Stomach	stomach
40	chr5:95231800-95237400	Weak transcription	Right Atrium	heart
41	chr5:95231800-95239600	Weak transcription	Left Ventricle	heart
42	chr5:95231800-95242200	Weak transcription	Pancreas	Pancrea
43	chr5:95231800-95242400	Weak transcription	Right Ventricle	heart
44	chr5:95231800-95243200	Weak transcription	Lung	lung
45	chr5:95231800-95244200	Weak transcription	Ovary	ovary
46	chr5:95232000-95238400	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr5:95232200-95244600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:95232400-95255200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr5:95232600-95237400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr5:95232600-95244600	Weak transcription	H1 Cell Line	embryonic stem cell

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