Variant report

Variant	rs56097641
Chromosome Location	chr15:77810740-77810741
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77809090..77810825-chr15:77820022..77822006,2	MCF-7	breast:
2	chr15:77800783..77803044-chr15:77808974..77810922,2	K562	blood:
3	chr15:77803142..77806483-chr15:77808853..77811512,3	K562	blood:
4	chr15:77801166..77802677-chr15:77810590..77812959,2	MCF-7	breast:
5	chr15:77800020..77805731-chr15:77808908..77813033,5	MCF-7	breast:
6	chr15:77318470..77320207-chr15:77810212..77811891,2	K562	blood:
7	chr15:77810042..77814304-chr15:77818656..77821099,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140368	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11856084	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11858844	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12324211	0.84[ASN][1000 genomes]
rs12324795	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16968897	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16968900	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17470952	0.84[EUR][1000 genomes]
rs17471431	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17471480	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17471697	0.87[EUR][1000 genomes]
rs17471753	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17472200	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2012740	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2012756	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2307141	0.87[EUR][1000 genomes]
rs2864840	0.87[EUR][1000 genomes]
rs3784788	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59204923	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59362734	0.87[EUR][1000 genomes]
rs59386622	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61306472	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74026910	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74026912	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74026913	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74026918	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74026923	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74026925	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74026926	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs907398	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56097641	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77800400-77819600	Weak transcription	Fetal Brain Female	brain
2	chr15:77801000-77818800	Weak transcription	Fetal Intestine Small	intestine
3	chr15:77801400-77820000	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:77801600-77821400	Weak transcription	Pancreas	Pancrea
5	chr15:77802600-77820000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:77803200-77819200	Weak transcription	Lung	lung
7	chr15:77803800-77811400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr15:77804000-77811200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:77804200-77819400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:77804200-77819800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:77807000-77810800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:77807400-77811000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:77807400-77819400	Weak transcription	Right Ventricle	heart
14	chr15:77807600-77819600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:77808000-77819000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:77808200-77811200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:77808200-77811800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:77808200-77819200	Weak transcription	Left Ventricle	heart
19	chr15:77808200-77820600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:77808600-77811000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:77808600-77813200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:77808600-77820000	Weak transcription	Brain Hippocampus Middle	brain
23	chr15:77808600-77821400	Weak transcription	Brain Anterior Caudate	brain
24	chr15:77808800-77811000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:77809200-77810800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:77809200-77812200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:77809200-77819400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:77810400-77811200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr15:77810400-77811600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:77810400-77811800	Enhancers	Spleen	Spleen
31	chr15:77810600-77811400	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr15:77810600-77811600	Enhancers	Placenta	Placenta
33	chr15:77810600-77811800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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