Variant report

Variant	rs3094579
Chromosome Location	chr6:29644308-29644309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs2535238	0.98[ASN][1000 genomes]
rs2535274	0.85[ASN][1000 genomes]
rs2535275	0.86[ASN][1000 genomes]
rs2747421	0.98[ASN][1000 genomes]
rs2747427	0.98[ASN][1000 genomes]
rs2747428	0.98[ASN][1000 genomes]
rs2747429	0.98[ASN][1000 genomes]
rs2747460	0.86[ASN][1000 genomes]
rs2907897	0.85[ASN][1000 genomes]
rs29218	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs29228	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3094724	0.82[ASN][1000 genomes]
rs3094725	0.83[ASN][1000 genomes]
rs3094730	0.81[ASN][1000 genomes]
rs3094731	0.81[ASN][1000 genomes]
rs3095266	0.83[ASN][1000 genomes]
rs3095269	0.92[ASN][1000 genomes]
rs3095271	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3095284	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3095290	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095294	0.87[ASN][1000 genomes]
rs3116811	0.81[ASN][1000 genomes]
rs3116814	0.84[ASN][1000 genomes]
rs3117289	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3117295	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3117299	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3117301	0.86[ASN][1000 genomes]
rs3117312	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3117318	0.92[ASN][1000 genomes]
rs3129033	0.84[ASN][1000 genomes]
rs3129035	0.84[ASN][1000 genomes]
rs3129039	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129046	0.81[ASN][1000 genomes]
rs3129058	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3129062	0.98[ASN][1000 genomes]
rs3129063	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3129067	0.81[ASN][1000 genomes]
rs3129069	0.92[ASN][1000 genomes]
rs3129073	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3129084	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129092	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130251	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3131867	0.81[ASN][1000 genomes]
rs3131895	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3131898	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs374317	0.98[ASN][1000 genomes]
rs375248	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs375984	0.98[ASN][1000 genomes]
rs376319	0.98[ASN][1000 genomes]
rs387640	0.98[ASN][1000 genomes]
rs387642	0.98[ASN][1000 genomes]
rs417764	0.98[ASN][1000 genomes]
rs448380	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs448489	0.98[ASN][1000 genomes]
rs9258017	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3094579	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs3094579	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3094579	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3094579	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29636600-29644800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:29637000-29644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:29638800-29644400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:29639600-29647400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:29643000-29646400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:29643000-29648800	Enhancers	HMEC	breast
8	chr6:29643200-29648400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:29643400-29648400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:29643600-29644600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:29643800-29644400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:29643800-29644600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:29643800-29644800	Enhancers	NHEK	skin
14	chr6:29643800-29647600	Enhancers	Fetal Heart	heart

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