Variant report

Variant	rs9646213
Chromosome Location	chr15:76807672-76807673
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76789083..76790896-chr15:76806122..76808106,2	MCF-7	breast:

Extended variants
information (count: 126 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10444858	0.82[ASN][1000 genomes]
rs11072599	0.81[AFR][1000 genomes]
rs11072603	0.84[ASN][1000 genomes]
rs1117367	0.84[ASN][1000 genomes]
rs1125932	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12148452	0.83[ASN][1000 genomes]
rs12148877	0.83[EUR][1000 genomes]
rs12437627	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12438077	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12438186	0.82[EUR][1000 genomes]
rs12438540	0.82[EUR][1000 genomes]
rs12440151	0.83[EUR][1000 genomes]
rs12440815	0.81[AFR][1000 genomes]
rs12441247	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441433	0.89[ASN][1000 genomes]
rs12441550	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12443137	0.85[ASN][1000 genomes]
rs12592171	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12592386	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12594541	0.90[ASN][1000 genomes]
rs12594577	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595313	0.83[ASN][1000 genomes]
rs12898430	0.84[ASN][1000 genomes]
rs12899871	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12900494	0.83[EUR][1000 genomes]
rs12902174	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12902414	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12902452	0.83[EUR][1000 genomes]
rs12907805	0.85[EUR][1000 genomes]
rs12908421	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914005	0.81[AFR][1000 genomes]
rs12916573	0.86[ASN][1000 genomes]
rs12917430	0.85[EUR][1000 genomes]
rs1588961	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17362383	0.83[EUR][1000 genomes]
rs17363713	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17364076	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17364330	0.81[AFR][1000 genomes]
rs17460201	0.85[EUR][1000 genomes]
rs17461634	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1838048	0.82[EUR][1000 genomes]
rs1867197	0.83[EUR][1000 genomes]
rs1874944	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1875885	0.81[AFR][1000 genomes]
rs1946650	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2056544	0.90[ASN][1000 genomes]
rs2117369	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2120107	0.84[ASN][1000 genomes]
rs2120108	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2164101	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2304920	0.83[ASN][1000 genomes]
rs2404736	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2404737	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2404740	0.85[ASN][1000 genomes]
rs2404741	0.84[ASN][1000 genomes]
rs284895	0.87[EUR][1000 genomes]
rs2896954	0.85[ASN][1000 genomes]
rs34060246	0.83[ASN][1000 genomes]
rs34287706	0.82[EUR][1000 genomes]
rs34478400	0.83[EUR][1000 genomes]
rs34707035	0.83[ASN][1000 genomes]
rs34924128	0.83[ASN][1000 genomes]
rs35077207	0.82[EUR][1000 genomes]
rs35138393	0.83[ASN][1000 genomes]
rs35195096	0.82[EUR][1000 genomes]
rs35395069	0.83[ASN][1000 genomes]
rs35498563	0.83[ASN][1000 genomes]
rs35566346	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816266	0.83[ASN][1000 genomes]
rs3866543	0.81[AFR][1000 genomes]
rs4079681	0.85[EUR][1000 genomes]
rs4525456	0.83[EUR][1000 genomes]
rs4886496	0.91[ASN][1000 genomes]
rs4886813	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886817	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886818	0.82[ASN][1000 genomes]
rs4886824	0.81[ASN][1000 genomes]
rs4886825	0.83[ASN][1000 genomes]
rs55676827	0.83[ASN][1000 genomes]
rs56089215	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56193230	0.82[EUR][1000 genomes]
rs56216512	0.85[EUR][1000 genomes]
rs56351018	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57178708	0.83[EUR][1000 genomes]
rs58361452	0.83[ASN][1000 genomes]
rs58511211	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58684938	0.84[EUR][1000 genomes]
rs58973160	0.83[ASN][1000 genomes]
rs59088060	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60912217	0.80[ASN][1000 genomes]
rs6495206	0.84[ASN][1000 genomes]
rs66754747	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66986092	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67010831	0.83[ASN][1000 genomes]
rs67204011	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67232575	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67263359	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67418609	0.81[AFR][1000 genomes]
rs67570291	0.83[ASN][1000 genomes]
rs67888330	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67920045	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71405216	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71405223	0.83[ASN][1000 genomes]
rs7162455	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7163397	0.82[EUR][1000 genomes]
rs7163946	0.81[AFR][1000 genomes]
rs7164060	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7164813	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7165025	0.81[AFR][1000 genomes]
rs7169394	0.82[EUR][1000 genomes]
rs7174953	0.83[EUR][1000 genomes]
rs7179142	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72738889	0.83[ASN][1000 genomes]
rs7342603	0.83[ASN][1000 genomes]
rs7350777	0.83[ASN][1000 genomes]
rs8024476	0.83[ASN][1000 genomes]
rs8025134	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8030411	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8039545	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8043057	0.81[EUR][1000 genomes]
rs8043474	0.83[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	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
5	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9646213	SCAPER	cis	Thyroid	GTEx
rs9646213	SCAPER	cis	lung	GTEx
rs9646213	SCAPER	cis	Artery Tibial	GTEx
rs9646213	SCAPER	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 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	chr15:76794000-76810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:76795800-76810600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:76797400-76825000	Weak transcription	Primary B cells from cord blood	blood
6	chr15:76804800-76808400	Enhancers	Fetal Intestine Small	intestine
7	chr15:76805000-76810200	Weak transcription	Fetal Heart	heart
8	chr15:76805200-76808400	Enhancers	Fetal Intestine Large	intestine
9	chr15:76805400-76810400	Weak transcription	Fetal Stomach	stomach
10	chr15:76805600-76808400	Enhancers	HepG2	liver
11	chr15:76805600-76845800	Weak transcription	Primary T cells from cord blood	blood
12	chr15:76806000-76807800	Enhancers	Duodenum Mucosa	Duodenum
13	chr15:76806000-76808400	Enhancers	Brain Germinal Matrix	brain
14	chr15:76806400-76808400	Enhancers	Liver	Liver
15	chr15:76806600-76808400	Enhancers	Small Intestine	intestine
16	chr15:76806600-76810400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:76807000-76810400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:76807200-76807800	Enhancers	Brain Hippocampus Middle	brain
19	chr15:76807200-76808000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr15:76807600-76807800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr15:76807600-76817800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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