Variant report

Variant	rs62007297
Chromosome Location	chr15:77709448-77709449
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	FOS	chr15:77709292-77709617	MCF10A-Er-Src	breast:	n/a	chr15:77709451-77709462
2	FOS	chr15:77709333-77709588	MCF10A-Er-Src	breast:	n/a	chr15:77709451-77709462
3	FOS	chr15:77709281-77709627	HUVEC	blood vessel:	n/a	chr15:77709451-77709462
4	FOS	chr15:77709316-77709595	MCF10A-Er-Src	breast:	n/a	chr15:77709451-77709462
5	JUND	chr15:77709298-77709617	K562	blood:	n/a	n/a
6	FOSL1	chr15:77709284-77709600	K562	blood:	n/a	n/a
7	FOS	chr15:77709294-77709617	MCF10A-Er-Src	breast:	n/a	chr15:77709451-77709462

No.	Distal block	Cell Line	Cell type
1	chr15:77709022..77711510-chr15:77717279..77719349,2	K562	blood:
2	chr15:77686365..77688021-chr15:77708534..77710284,2	K562	blood:
3	chr15:77701664..77703699-chr15:77708996..77711356,2	MCF-7	breast:
4	chr15:77688577..77690434-chr15:77709040..77711857,2	K562	blood:
5	chr15:77700084..77701630-chr15:77707595..77709456,2	K562	blood:

Variant related genes	Relation type
HMG20A	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10162778	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11853696	0.88[ASN][1000 genomes]
rs11856084	0.86[ASN][1000 genomes]
rs11858844	0.83[ASN][1000 genomes]
rs12324016	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12324211	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12324795	0.89[ASN][1000 genomes]
rs12912084	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13380202	0.88[ASN][1000 genomes]
rs1493699	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16968799	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17384809	0.88[ASN][1000 genomes]
rs17385059	0.88[ASN][1000 genomes]
rs17385296	0.88[ASN][1000 genomes]
rs17385352	0.88[ASN][1000 genomes]
rs17470529	0.90[ASN][1000 genomes]
rs17470952	0.90[ASN][1000 genomes]
rs17471252	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17471431	0.86[ASN][1000 genomes]
rs17471480	0.86[ASN][1000 genomes]
rs17471697	0.84[ASN][1000 genomes]
rs17471753	0.84[ASN][1000 genomes]
rs2012740	0.87[ASN][1000 genomes]
rs2012756	0.87[ASN][1000 genomes]
rs2172587	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307141	0.86[ASN][1000 genomes]
rs28437977	0.90[ASN][1000 genomes]
rs2864840	0.91[ASN][1000 genomes]
rs35651077	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784787	0.90[ASN][1000 genomes]
rs3784788	0.84[ASN][1000 genomes]
rs4886863	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886864	0.90[ASN][1000 genomes]
rs4886865	0.90[ASN][1000 genomes]
rs59362734	0.85[ASN][1000 genomes]
rs59386622	0.86[ASN][1000 genomes]
rs62010566	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74026910	0.88[ASN][1000 genomes]
rs74026912	0.90[ASN][1000 genomes]
rs74026913	0.91[ASN][1000 genomes]
rs74026918	0.84[ASN][1000 genomes]
rs74026923	0.83[ASN][1000 genomes]
rs74026926	0.84[ASN][1000 genomes]
rs8029163	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8035526	0.90[ASN][1000 genomes]
rs883627	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs907398	0.83[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	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv21291	chr15:77707945-77712363	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62007297	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77698600-77711200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:77702600-77711000	Weak transcription	Lung	lung
3	chr15:77702800-77711000	Weak transcription	Aorta	Aorta
4	chr15:77703000-77711400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:77703200-77710800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:77703400-77710000	Weak transcription	Thymus	Thymus
7	chr15:77704400-77709800	Weak transcription	HepG2	liver
8	chr15:77704400-77710000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:77704800-77710800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:77706400-77709800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:77706600-77710400	Weak transcription	Stomach Mucosa	stomach
12	chr15:77707200-77709600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:77707200-77710600	Enhancers	Fetal Heart	heart
14	chr15:77707200-77710800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr15:77707600-77709600	Enhancers	HUVEC	blood vessel
16	chr15:77707600-77710200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr15:77707600-77710200	Enhancers	Psoas Muscle	Psoas
18	chr15:77707600-77710400	Enhancers	Right Ventricle	heart
19	chr15:77707600-77710600	Enhancers	Ovary	ovary
20	chr15:77707800-77709800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:77707800-77709800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr15:77707800-77710000	Enhancers	Fetal Lung	lung
23	chr15:77707800-77710600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:77707800-77710600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:77707800-77710800	Enhancers	Brain Hippocampus Middle	brain
26	chr15:77707800-77711000	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr15:77708000-77710000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr15:77708000-77710200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr15:77708000-77710400	Enhancers	Brain Anterior Caudate	brain
30	chr15:77708000-77710600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:77708000-77710600	Enhancers	Fetal Muscle Leg	muscle
32	chr15:77708000-77710800	Weak transcription	Placenta	Placenta
33	chr15:77708200-77709600	Enhancers	Liver	Liver
34	chr15:77708200-77710000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr15:77708200-77710200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr15:77708200-77710200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:77708200-77710200	Weak transcription	GM12878-XiMat	blood
38	chr15:77708200-77710400	Weak transcription	Primary T cells from cord blood	blood
39	chr15:77708200-77710600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:77708200-77710800	Enhancers	HSMM	muscle
41	chr15:77708200-77711400	Weak transcription	Gastric	stomach
42	chr15:77708200-77711400	Weak transcription	Pancreas	Pancrea
43	chr15:77708200-77711400	Weak transcription	Spleen	Spleen
44	chr15:77708400-77710600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:77708400-77710600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:77708400-77710800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr15:77708400-77711200	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr15:77708600-77710000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:77708600-77710200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:77708600-77710400	Enhancers	K562	blood

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