Variant report

Variant	rs6494079
Chromosome Location	chr15:59521613-59521614
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	POLR2A	chr15:59520777-59521622	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:59521150-59521639	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:59521078-59521617	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
MYO1E	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs3794488	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774323	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57487429	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58579379	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59773793	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62002697	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494080	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6494084	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494086	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494087	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6494089	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7167255	0.87[AFR][1000 genomes]
rs7172489	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172761	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7174147	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7175876	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179352	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7181249	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027055	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8027766	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8038705	0.90[EUR][1000 genomes]
rs8040147	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv904272	chr15:59500577-59549018	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv904273	chr15:59518488-59567137	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59467800-59523200	Weak transcription	Fetal Brain Female	brain
2	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
3	chr15:59487800-59524400	Weak transcription	Small Intestine	intestine
4	chr15:59493200-59523200	Strong transcription	Hela-S3	cervix
5	chr15:59496800-59522000	Strong transcription	NHEK	skin
6	chr15:59497000-59524800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:59498800-59522000	Strong transcription	GM12878-XiMat	blood
8	chr15:59500000-59524400	Weak transcription	Right Ventricle	heart
9	chr15:59500600-59524600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:59501200-59523400	Weak transcription	Ovary	ovary
11	chr15:59501200-59525600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:59502800-59525800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:59511400-59549200	Weak transcription	Colonic Mucosa	Colon
14	chr15:59514800-59524200	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:59515000-59524400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:59515400-59523800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:59515800-59522000	Strong transcription	HMEC	breast
18	chr15:59515800-59566600	Weak transcription	Pancreas	Pancrea
19	chr15:59516400-59522800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:59516400-59524600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:59516600-59524400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:59516600-59529400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:59516800-59522800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:59516800-59523200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr15:59517000-59524200	Strong transcription	HSMM	muscle
26	chr15:59517000-59530200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:59517000-59536600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr15:59517200-59523200	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:59517200-59523200	Weak transcription	Gastric	stomach
30	chr15:59517200-59523200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:59517200-59524400	Weak transcription	Aorta	Aorta
32	chr15:59517200-59524400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:59517200-59528600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr15:59517200-59528800	Weak transcription	Primary B cells from cord blood	blood
35	chr15:59517200-59529000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:59517400-59523000	Weak transcription	Brain Substantia Nigra	brain
37	chr15:59517400-59523400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:59517400-59524600	Weak transcription	Fetal Heart	heart
39	chr15:59517400-59529000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:59517400-59530000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:59517600-59523200	Weak transcription	NHLF	lung
42	chr15:59517600-59523400	Weak transcription	Adipose Nuclei	Adipose
43	chr15:59517600-59523800	Weak transcription	Lung	lung
44	chr15:59517600-59524600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr15:59517600-59525000	Weak transcription	Spleen	Spleen
46	chr15:59517600-59528600	Weak transcription	HepG2	liver
47	chr15:59517600-59529000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:59517600-59546400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr15:59517800-59523400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:59517800-59524200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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