Variant report

Variant	rs1104815
Chromosome Location	chr15:77865046-77865047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77864365..77867025-chr15:77869640..77872108,2	MCF-7	breast:
2	chr15:77856989..77859495-chr15:77861940..77865382,3	K562	blood:
3	chr15:77860363..77863668-chr15:77864267..77867089,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMG20A-2	chr15:77864907-77865206	ENSG00000259420.1
2	lnc-HMG20A-2	chr15:77864907-77865081	ENSG00000259420.1

Variant related genes	Relation type
ENSG00000259420	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11630235	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11630856	0.89[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11631894	0.89[EUR][1000 genomes]
rs11633811	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs11635834	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11638674	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs12593629	0.80[ASN][1000 genomes]
rs16968998	0.94[CEU][hapmap]
rs16968999	0.94[CEU][hapmap]
rs2003883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2667757	0.81[ASN][1000 genomes]
rs4286073	0.88[EUR][1000 genomes]
rs4886517	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886879	0.88[AMR][1000 genomes]
rs4886880	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886882	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4886884	0.82[EUR][1000 genomes]
rs4886885	0.82[EUR][1000 genomes]
rs4886886	0.82[EUR][1000 genomes]
rs4886887	0.94[CEU][hapmap]
rs4886888	0.94[CEU][hapmap]
rs7170855	0.80[ASN][1000 genomes]
rs7171141	0.88[EUR][1000 genomes]
rs8039399	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs8040227	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs868298	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs964990	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1104815	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77862000-77869400	Weak transcription	Brain Anterior Caudate	brain
2	chr15:77862200-77868200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr15:77862200-77869000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:77862200-77875000	Weak transcription	Left Ventricle	heart
5	chr15:77862400-77865800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:77862400-77866600	Weak transcription	Lung	lung
7	chr15:77862400-77867200	Weak transcription	Stomach Mucosa	stomach
8	chr15:77862400-77868000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:77862400-77868800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:77862400-77869400	Weak transcription	Brain Angular Gyrus	brain
11	chr15:77862400-77869400	Weak transcription	Brain Substantia Nigra	brain
12	chr15:77862600-77865800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:77862600-77868000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:77862600-77869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:77862800-77865600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:77862800-77867800	Weak transcription	Fetal Intestine Small	intestine
17	chr15:77862800-77868400	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:77862800-77869600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:77864000-77869600	Weak transcription	Fetal Stomach	stomach
20	chr15:77864000-77871400	Weak transcription	Spleen	Spleen
21	chr15:77864400-77866000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:77864800-77865200	Enhancers	Fetal Muscle Trunk	muscle
23	chr15:77864800-77865600	Enhancers	Placenta	Placenta
24	chr15:77864800-77866600	Enhancers	Brain Hippocampus Middle	brain
25	chr15:77865000-77866200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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