Variant report

Variant	rs12594212
Chromosome Location	chr15:76802014-76802015
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11072599	0.83[ASN][1000 genomes]
rs11072603	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1117367	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12148786	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148805	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441433	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12443137	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592171	0.83[ASN][1000 genomes]
rs12593751	0.84[ASN][1000 genomes]
rs12594541	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12898430	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12899871	0.85[ASN][1000 genomes]
rs12902414	0.91[ASN][1000 genomes]
rs12914005	0.85[ASN][1000 genomes]
rs12915248	0.85[ASN][1000 genomes]
rs12916573	0.91[ASN][1000 genomes]
rs1587381	0.85[ASN][1000 genomes]
rs1588961	0.85[ASN][1000 genomes]
rs17363713	0.84[ASN][1000 genomes]
rs17364076	0.85[ASN][1000 genomes]
rs17364330	0.85[ASN][1000 genomes]
rs17461634	0.85[ASN][1000 genomes]
rs1838050	0.81[EUR][1000 genomes]
rs1965492	0.82[ASN][1000 genomes]
rs2056544	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2083762	0.83[EUR][1000 genomes]
rs2117369	0.85[ASN][1000 genomes]
rs2120107	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2164101	0.85[ASN][1000 genomes]
rs2404740	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2404741	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs284895	0.85[ASN][1000 genomes]
rs2896954	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4633676	0.82[ASN][1000 genomes]
rs4886818	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56089215	0.82[ASN][1000 genomes]
rs6495206	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66986092	0.91[ASN][1000 genomes]
rs67232575	0.84[ASN][1000 genomes]
rs67263359	0.91[ASN][1000 genomes]
rs67888330	0.84[ASN][1000 genomes]
rs67920045	0.91[ASN][1000 genomes]
rs7162455	0.82[ASN][1000 genomes]
rs7163946	0.85[ASN][1000 genomes]
rs7165025	0.85[ASN][1000 genomes]
rs8025134	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12594212	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs12594212	SCAPER	cis	Thyroid	GTEx
rs12594212	SCAPER	cis	Artery Tibial	GTEx
rs12594212	SCAPER	cis	lung	GTEx
rs12594212	SCAPER	cis	Nerve Tibial	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76725800-76812600	Weak transcription	Left Ventricle	heart
2	chr15:76788400-76813600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr15:76791200-76806200	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:76794000-76810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:76794200-76806400	Weak transcription	Gastric	stomach
6	chr15:76795200-76806800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:76795800-76810600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:76796400-76805200	Weak transcription	Fetal Intestine Large	intestine
9	chr15:76796800-76806400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:76797000-76805000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:76797000-76806400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:76797200-76803600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:76797200-76804800	Weak transcription	Primary T cells from cord blood	blood
14	chr15:76797200-76806400	Weak transcription	Liver	Liver
15	chr15:76797400-76825000	Weak transcription	Primary B cells from cord blood	blood
16	chr15:76799800-76804800	Weak transcription	Fetal Intestine Small	intestine
17	chr15:76800400-76806000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:76801000-76804600	Weak transcription	Fetal Heart	heart

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