Variant report

Variant	rs62016940
Chromosome Location	chr15:50717923-50717924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr15:50717898-50718158	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50644978..50654282-chr15:50714279..50723145,48	MCF-7	breast:
2	chr15:50644601..50650486-chr15:50714318..50720349,10	K562	blood:
3	chr15:50714855..50718759-chr15:50728296..50731650,9	MCF-7	breast:
4	chr15:50644770..50653815-chr15:50713287..50720249,51	MCF-7	breast:
5	chr15:50644809..50652796-chr15:50713240..50720627,20	K562	blood:
6	chr15:50715057..50718112-chr15:51199966..51202837,4	MCF-7	breast:
7	chr15:50716224..50718029-chr15:52121423..52123385,2	MCF-7	breast:

No data

Variant related genes	Relation type
USP8	TF binding region
ENSG00000264109	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000259715	Chromatin interaction
ENSG00000081014	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10519276	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519278	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11070774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070775	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070777	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070778	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070779	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070780	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070781	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070785	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11070786	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11070787	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11070788	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11630309	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11631351	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11631398	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11632697	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11632708	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11632823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11633608	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11633624	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11633765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11634832	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11637031	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11637104	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11637111	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11638198	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11638390	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12439248	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12440152	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17519466	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17519536	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17597852	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17597915	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17598061	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414045	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34659874	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4380013	0.84[EUR][1000 genomes]
rs4774569	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4774570	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4774571	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4774572	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775883	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775884	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775885	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775886	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775888	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775889	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62016938	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016942	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016943	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019074	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019075	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019076	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019077	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019078	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62019079	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019080	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019082	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019084	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019085	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019087	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62019112	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62019113	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62019115	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62019116	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62019117	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7165464	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168783	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7169778	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7170114	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7181536	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7182569	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182980	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7494907	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8030373	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8037446	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8037553	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs934636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv524613	chr15:50656449-50868779	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv904210	chr15:50702058-50786024	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1040717	chr15:50715572-50846521	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1053966	chr15:50715572-51133186	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv542383	chr15:50715572-51133186	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50715600-50718000	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr15:50715600-50718400	Active TSS	Hela-S3	cervix
3	chr15:50715800-50718000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr15:50715800-50718000	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr15:50715800-50718200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:50715800-50718200	Active TSS	Colonic Mucosa	Colon
7	chr15:50715800-50718200	Active TSS	Right Atrium	heart
8	chr15:50715800-50718400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:50715800-50718400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:50715800-50718400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:50716000-50718000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:50716000-50718000	Active TSS	Fetal Intestine Large	intestine
13	chr15:50716000-50718000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr15:50716000-50718600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:50716000-50718600	Active TSS	K562	blood
16	chr15:50716200-50718000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:50716200-50718000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:50716200-50718000	Active TSS	NHDF-Ad	bronchial
19	chr15:50716200-50718200	Active TSS	HMEC	breast
20	chr15:50716200-50719200	Active TSS	GM12878-XiMat	blood
21	chr15:50716800-50718800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr15:50717000-50718000	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr15:50717000-50718200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr15:50717000-50718200	Flanking Active TSS	Liver	Liver
25	chr15:50717000-50718600	Weak transcription	Spleen	Spleen
26	chr15:50717000-50726800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:50717200-50718000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:50717200-50718000	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr15:50717200-50718000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:50717200-50718000	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr15:50717200-50718000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr15:50717200-50718000	Flanking Active TSS	Fetal Brain Male	brain
33	chr15:50717200-50718000	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr15:50717200-50718000	Flanking Active TSS	HUVEC	blood vessel
35	chr15:50717200-50718000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr15:50717200-50718200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:50717200-50718200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr15:50717200-50718200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:50717200-50718200	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr15:50717400-50718000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr15:50717400-50718000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:50717400-50718000	Flanking Active TSS	Fetal Lung	lung
43	chr15:50717400-50718000	Weak transcription	Pancreas	Pancrea
44	chr15:50717400-50718000	Flanking Active TSS	Dnd41	blood
45	chr15:50717400-50718000	Flanking Active TSS	Osteobl	bone
46	chr15:50717400-50718600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr15:50717400-50722600	Weak transcription	Esophagus	oesophagus
48	chr15:50717400-50722600	Weak transcription	Lung	lung
49	chr15:50717400-50747000	Weak transcription	Aorta	Aorta
50	chr15:50717600-50718000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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