Variant report

Variant	rs6703576
Chromosome Location	chr1:86841737-86841738
allele	A/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	EBF1	chr1:86841413-86841763	GM12878	blood:	n/a	chr1:86841593-86841604

Variant related genes	Relation type
ODF2L	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10158226	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10782571	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873771	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10873772	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873773	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873774	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873775	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873776	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873779	0.96[EUR][1000 genomes]
rs1116108	0.97[EUR][1000 genomes]
rs1116109	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161803	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161804	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161805	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161806	0.97[EUR][1000 genomes]
rs11161807	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161811	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161813	0.95[EUR][1000 genomes]
rs11799437	0.97[EUR][1000 genomes]
rs11802019	0.95[EUR][1000 genomes]
rs11810689	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028714	0.97[EUR][1000 genomes]
rs12031536	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12033867	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12036110	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12046485	0.97[EUR][1000 genomes]
rs12072655	0.94[ASN][1000 genomes]
rs12131620	0.96[EUR][1000 genomes]
rs12138401	0.94[EUR][1000 genomes]
rs1407719	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407720	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413427	0.94[ASN][1000 genomes]
rs1413429	0.92[ASN][1000 genomes]
rs16908	0.81[ASN][1000 genomes]
rs17372196	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1830675	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1999600	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2031136	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2093612	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2181418	0.99[ASN][1000 genomes]
rs2210641	0.94[ASN][1000 genomes]
rs2273941	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273942	0.97[EUR][1000 genomes]
rs2275000	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2390096	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2390097	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2390098	0.96[EUR][1000 genomes]
rs2390099	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28782251	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35173920	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3737159	0.91[ASN][1000 genomes]
rs3737672	0.92[EUR][1000 genomes]
rs3945233	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4534352	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4638096	0.95[EUR][1000 genomes]
rs4656026	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656044	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656064	0.96[EUR][1000 genomes]
rs4656066	0.94[EUR][1000 genomes]
rs58200516	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658025	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674140	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6679600	0.97[EUR][1000 genomes]
rs6683267	0.96[EUR][1000 genomes]
rs67799288	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415758	0.92[ASN][1000 genomes]
rs7515651	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7541004	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7553685	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7554545	0.96[EUR][1000 genomes]
rs956499	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1793594	chr1:86833653-86858957	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6703576	ODF2L	cis	Nerve Tibial	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86808600-86842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:86813800-86842600	Weak transcription	Fetal Heart	heart
3	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
4	chr1:86816000-86842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:86817200-86843800	Weak transcription	Small Intestine	intestine
6	chr1:86817600-86843000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:86817800-86842400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:86818000-86842600	Weak transcription	Fetal Intestine Small	intestine
9	chr1:86818000-86843200	Weak transcription	Pancreas	Pancrea
10	chr1:86818000-86851600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:86819800-86842200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:86819800-86842600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:86819800-86843000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:86819800-86843000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:86820200-86842600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:86820200-86843400	Weak transcription	Left Ventricle	heart
17	chr1:86820200-86854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:86820200-86854800	Weak transcription	HSMMtube	muscle
19	chr1:86820400-86842400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:86820400-86842800	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:86820400-86842800	Weak transcription	Placenta	Placenta
22	chr1:86820400-86845400	Weak transcription	Hela-S3	cervix
23	chr1:86820400-86846200	Weak transcription	NHLF	lung
24	chr1:86820400-86846400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:86820400-86847000	Weak transcription	Liver	Liver
26	chr1:86820400-86848000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:86820400-86860200	Weak transcription	NHEK	skin
28	chr1:86820600-86842800	Weak transcription	Brain Substantia Nigra	brain
29	chr1:86820600-86843000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:86820600-86848000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:86820800-86842000	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:86822400-86846200	Weak transcription	Gastric	stomach
33	chr1:86823000-86843000	Weak transcription	Ovary	ovary
34	chr1:86824000-86843000	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:86824000-86848200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:86825600-86842800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:86826400-86842800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:86828800-86842800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:86828800-86842800	Weak transcription	Fetal Stomach	stomach
40	chr1:86829200-86842800	Weak transcription	Fetal Brain Female	brain
41	chr1:86836400-86842800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:86836600-86860800	Weak transcription	Aorta	Aorta
43	chr1:86837200-86842800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:86838200-86842000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:86838200-86842800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:86838200-86843600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:86838200-86845800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:86838400-86842000	Strong transcription	NHDF-Ad	bronchial
49	chr1:86838400-86842400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:86838400-86842400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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