Variant report

Variant	rs6825241
Chromosome Location	chr4:152543783-152543784
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10007015	0.82[EUR][1000 genomes]
rs10007167	0.82[EUR][1000 genomes]
rs10019048	0.82[EUR][1000 genomes]
rs10776524	0.82[EUR][1000 genomes]
rs1105534	0.82[EUR][1000 genomes]
rs1105535	0.82[EUR][1000 genomes]
rs1105536	0.82[EUR][1000 genomes]
rs12502055	0.82[EUR][1000 genomes]
rs12647555	0.81[CHB][hapmap]
rs1366909	0.82[EUR][1000 genomes]
rs1372976	0.81[CHB][hapmap]
rs1372977	0.86[CHB][hapmap]
rs1372978	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1443087	0.81[CHB][hapmap]
rs1443088	0.81[CHB][hapmap]
rs1443089	0.81[CHB][hapmap]
rs1443094	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1470280	0.81[CHB][hapmap]
rs1561915	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17027798	0.80[EUR][1000 genomes]
rs1877187	0.81[EUR][1000 genomes]
rs1896883	0.80[EUR][1000 genomes]
rs1946999	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2007445	0.82[EUR][1000 genomes]
rs2053566	0.81[CHB][hapmap]
rs2709828	0.81[CHB][hapmap]
rs2709831	0.81[CHB][hapmap]
rs2724567	0.81[CHB][hapmap]
rs2724577	0.81[CHB][hapmap]
rs2840130	0.82[EUR][1000 genomes]
rs28665936	0.80[AFR][1000 genomes]
rs3749563	0.80[EUR][1000 genomes]
rs4263379	0.81[CHB][hapmap]
rs4571	0.80[EUR][1000 genomes]
rs4696099	0.88[GIH][hapmap]
rs4696104	0.82[EUR][1000 genomes]
rs4696277	0.87[EUR][1000 genomes]
rs4696284	0.82[EUR][1000 genomes]
rs4696285	0.82[EUR][1000 genomes]
rs55668815	0.80[EUR][1000 genomes]
rs6535809	0.82[EUR][1000 genomes]
rs6535811	0.82[EUR][1000 genomes]
rs6535812	0.82[EUR][1000 genomes]
rs6535813	0.82[EUR][1000 genomes]
rs6810860	0.82[EUR][1000 genomes]
rs6814554	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6817058	0.82[EUR][1000 genomes]
rs6818667	0.81[EUR][1000 genomes]
rs6823002	0.81[EUR][1000 genomes]
rs6823194	0.81[EUR][1000 genomes]
rs6823421	0.82[EUR][1000 genomes]
rs6823423	0.82[EUR][1000 genomes]
rs6826799	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6832562	0.82[EUR][1000 genomes]
rs6833368	0.82[EUR][1000 genomes]
rs6834095	0.82[EUR][1000 genomes]
rs6838966	0.82[EUR][1000 genomes]
rs6839074	0.82[EUR][1000 genomes]
rs6840360	0.81[EUR][1000 genomes]
rs6840678	0.81[EUR][1000 genomes]
rs6841204	0.82[EUR][1000 genomes]
rs6841783	0.82[EUR][1000 genomes]
rs6845944	0.81[EUR][1000 genomes]
rs6846114	0.81[EUR][1000 genomes]
rs6849050	0.82[EUR][1000 genomes]
rs73862064	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7439465	0.80[EUR][1000 genomes]
rs749982	0.82[EUR][1000 genomes]
rs751012	0.82[EUR][1000 genomes]
rs751014	0.82[EUR][1000 genomes]
rs7671651	0.80[EUR][1000 genomes]
rs7695162	0.84[EUR][1000 genomes]
rs7695412	0.88[GIH][hapmap]
rs907237	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv881342	chr4:152363772-152560449	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830114	chr4:152401288-152548606	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6825241	SH3D19	cis	cerebellum	SCAN
rs6825241	PET112L	cis	parietal	SCAN
rs6825241	PET112L	cis	multi-tissue	Pritchard
rs6825241	FAM160A1	cis	Whole Blood	GTEx
rs6825241	PET112L	cis	cerebellum	SCAN
rs6825241	PET112L	cis	lymphoblastoid	seeQTL
rs6825241	FAM160A1	cis	parietal	SCAN
rs6825241	FAM160A1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152499200-152567600	Weak transcription	Pancreas	Pancrea
2	chr4:152521600-152546200	Weak transcription	Right Ventricle	heart
3	chr4:152522400-152548400	Weak transcription	NHEK	skin
4	chr4:152522400-152560200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:152522600-152548400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:152525600-152544200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:152528400-152548600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:152537200-152545400	Weak transcription	Right Atrium	heart
9	chr4:152539400-152544000	Weak transcription	Fetal Heart	heart
10	chr4:152540400-152545400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:152540400-152545400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:152540400-152546200	Weak transcription	Psoas Muscle	Psoas
13	chr4:152540800-152544200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr4:152542000-152544400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr4:152542200-152544000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr4:152542200-152544000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr4:152542400-152543800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr4:152542400-152565600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:152542600-152545400	Weak transcription	Fetal Brain Male	brain
20	chr4:152543000-152543800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr4:152543200-152543800	Enhancers	H9 Cell Line	embryonic stem cell
22	chr4:152543200-152544000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr4:152543200-152544400	Enhancers	HepG2	liver

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