Variant report

Variant	rs28706124
Chromosome Location	chr15:77896237-77896238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77862030..77863568-chr15:77895689..77897664,2	MCF-7	breast:
2	chr15:77890507..77893828-chr15:77894009..77899298,4	MCF-7	breast:
3	chr15:77895225..77896761-chr15:77915510..77917012,2	K562	blood:
4	chr15:77891327..77896574-chr15:77898422..77902980,9	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11631894	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11636780	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638351	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638674	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16968998	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968999	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28368579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477219	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4286073	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886882	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886884	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4886885	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4886886	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4886887	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886888	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171141	0.87[EUR][1000 genomes]
rs884527	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9806139	0.98[AMR][1000 genomes];0.97[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	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	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
3	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv904417	chr15:77851535-77935992	Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904418	chr15:77851535-77963887	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1036749	chr15:77884026-77912408	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28706124	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77889800-77896400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:77891000-77896600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:77891000-77898800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:77892200-77897200	Weak transcription	Gastric	stomach
5	chr15:77892200-77897600	Weak transcription	Right Ventricle	heart
6	chr15:77892400-77896800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:77892400-77896800	Weak transcription	Lung	lung
8	chr15:77892400-77897000	Weak transcription	Right Atrium	heart
9	chr15:77892800-77896400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:77892800-77896600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:77892800-77897000	Weak transcription	Fetal Thymus	thymus
12	chr15:77892800-77897200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:77893000-77896400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr15:77893000-77896400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:77893000-77896600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:77893000-77896800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr15:77893200-77897200	Weak transcription	K562	blood
18	chr15:77894000-77896400	Weak transcription	Spleen	Spleen
19	chr15:77895000-77898600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:77895800-77896400	Enhancers	Left Ventricle	heart
21	chr15:77895800-77896600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:77895800-77897000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr15:77895800-77897000	Enhancers	Brain Anterior Caudate	brain
24	chr15:77895800-77899800	Enhancers	Fetal Heart	heart
25	chr15:77895800-77901200	Enhancers	Fetal Muscle Leg	muscle
26	chr15:77896000-77896600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:77896000-77896600	Enhancers	Brain Substantia Nigra	brain
28	chr15:77896000-77896600	Enhancers	Fetal Muscle Trunk	muscle
29	chr15:77896000-77897000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:77896000-77897000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:77896000-77897000	Enhancers	Brain Cingulate Gyrus	brain
32	chr15:77896000-77897000	Enhancers	Brain Hippocampus Middle	brain
33	chr15:77896000-77897000	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr15:77896000-77897200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:77896000-77897200	Enhancers	Fetal Brain Male	brain
36	chr15:77896200-77896600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr15:77896200-77897000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:77896200-77897000	Enhancers	Brain Angular Gyrus	brain
39	chr15:77896200-77897800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr15:77896200-77897800	Enhancers	Fetal Lung	lung
41	chr15:77896200-77898000	Enhancers	Fetal Stomach	stomach
42	chr15:77896200-77900400	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr15:77896200-77900600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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